diff --git a/scripts/utilities/intervals/create_scatter_intervals.py b/scripts/utilities/intervals/create_scatter_intervals.py new file mode 100644 index 0000000..ec6091f --- /dev/null +++ b/scripts/utilities/intervals/create_scatter_intervals.py @@ -0,0 +1,190 @@ +# usr/bin/python + +###################################################################################### +# This script creates interval subset lists from a master list for scattering N-ways +# +# Usage: +# python create_scatter_intervals.py \ +# demo.interval_list 50 4 output_intervals "demo intervals scattered 50-ways" +# +###################################################################################### + +# INPUT REQUIREMENTS +# +# The script assumes that the master interval list is formatted according to +# Picard conventions as defined below: +# +# Picard-style interval files have a SAM-like header that includes a sequence +# dictionary. The intervals are given in the form of: +# +# + +# +# with fields separated by tabs, and the coordinates are 1-based (first position +# in the genome is position 1, not position 0). +# +# Example: +# +# @HD VN:1.0 SO:coordinate +# @SQ SN:1 LN:249250621 AS:GRCh37 [UR:. M5:. SP:.] +# @SQ SN:2 LN:243199373 AS:GRCh37 [UR:. M5:. SP:.] +# 1 30366 30503 + target_1 +# 1 69089 70010 + target_2 +# 1 367657 368599 + target_3 + +# LOGIC +# +# The script attempts to partition the intervals in the master list into N subsets +# of consecutive intervals (set by "desired_N"), balanced so that the subsets all +# add up to roughly the same amount of genomic territory. Based on the desired N and +# the "wiggle_factor" value, the script defines a maximum length of territory allowed +# per subset. It then iterates through all intervals, creating subsets and adding +# intervals until the max size is exceeded and a new subset is warranted. +# +# Note that depending on the master intervals, the wiggle factor may need to be tweaked +# in order to achieve exactly N subsets. + +# OUTPUT +# +# The script outputs a set of Picard-style interval files in the requested directory +# as well as a JSON stub file that can be used as base list for a WDL's inputs JSON. + + +import os +import sys + +# CLI arguments +master_list_file = sys.argv[1] +desired_N = int(sys.argv[2]) +wiggle_factor = int(sys.argv[3]) +dir_name = sys.argv[4] +comment = "@CO\t"+sys.argv[5]+"\n" + +# Read in the master list file contents: +with open(master_list_file, "r") as master_list: + + header_lines = [] + intervals_list = [] + longest_interval = 0 + + for line in master_list: + # store the header lines (starting with @) to serve as output stub + if line.startswith("@"): + header_lines.append(line) + else: + line_split = line.split("\t") + length = int(line_split[2])-int(line_split[1]) + intervals_list.append((line, length)) + + # keep track of what is the longest interval + if length > longest_interval: + longest_interval = length + +print "Number of intervals: "+str(len(intervals_list)) +print "Longest interval was: "+str(longest_interval) + +# Determine what is the total territory covered by intervals +total_length = 0 +for interval in intervals_list: + total_length = total_length + interval[1] + +print "Total length of covered territory: "+str(total_length) + +# Determine what should be the theoretical maximum territory per subset +# based on the desired N +max_length_per_subset = total_length / desired_N + +print "Theoretical max subset length: "+str(max_length_per_subset) + +# Distribute intervals to separate files + +interval_count = 0 +batch_count = 0 +current_batch = [] +current_length = 0 +length_so_far = 0 +batches_list = [] + +print "Processing..." + +def dump_batch(msg): + + global batch_count + global current_batch + global current_length + global length_so_far + global interval_count + global batches_list + + # increment appropriate counters + batch_count +=1 + length_so_far = length_so_far + current_length + # report batch stats + print "\t"+str(batch_count)+". \tBatch of "+str(len(current_batch))+"\t| "+str(current_length)+" \t|"+msg+" \t| "+str(interval_count)+" \t| So far "+str(length_so_far)+" \t| Remains "+str(total_length-length_so_far) + # store batch + batches_list.append(current_batch) + # reset everything + current_batch = [] + current_length = 0 + +for interval in intervals_list: + + interval_count +=1 + #print interval_count + + # Is this new interval above the length limit by itself? + if interval[1] > max_length_per_subset: + dump_batch("close-out") + current_batch.append(interval) + current_length = current_length + interval[1] + dump_batch("godzilla") + + # Is this new interval putting us above the length limit when added to the batch? + elif current_length + interval[1] > max_length_per_subset+max_length_per_subset/wiggle_factor: + dump_batch("normal") + current_batch.append(interval) + current_length = current_length + interval[1] + + else: + current_batch.append(interval) + current_length = current_length + interval[1] + +dump_batch("finalize") + +print "Done.\nGrouped intervals into "+str(len(batches_list))+" batches." + +# Write batches to files and compose a JSON stub +counter = 0 +json_stub = ["{", "\t\"workflow.scattered_calling_intervals\": ["] +os.mkdir(dir_name) +for batch in batches_list: + counter +=1 + path = dir_name+"/"+str(counter)+"_of_"+str(len(batches_list)) + os.mkdir(path) + with open(path+"/scattered.interval_list", "w") as intervals_file: + # Write out the header copied from the original + for line in header_lines: + intervals_file.write("%s" % line) + # Add a comment to the header + intervals_file.write("%s" % comment) + # Write out the intervals + for interval in batch: + intervals_file.write("%s" % interval[0]) + + # add the json line + json_stub.append("\t\t\"gs://bucket/dir/"+path+"/scattered.interval_list\",") +json_stub.append("\t]") +json_stub.append("}") + +print "Wrote "+str(counter)+" interval files to \""+dir_name+"/n_of_N/scattered.interval_list\"" + +# Write out the json stub +with open("scattered_intervals.json", "w") as json_file: + for line in json_stub: + json_file.write("%s\n" % line) + +print "Wrote a JSON stub to \"scattered_intervals.json\"" + + + + + diff --git a/scripts/utilities/intervals/create_scatter_intervals_demo/demo.interval_list b/scripts/utilities/intervals/create_scatter_intervals_demo/demo.interval_list new file mode 100644 index 0000000..0a3d0db --- /dev/null +++ b/scripts/utilities/intervals/create_scatter_intervals_demo/demo.interval_list @@ -0,0 +1,714 @@ +@HD VN:1.4 SO:coordinate +@SQ SN:1 LN:249250621 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Homo 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new file mode 100644 index 0000000..b771e03 --- /dev/null +++ b/scripts/utilities/intervals/create_scatter_intervals_demo/demo_stdout.txt @@ -0,0 +1,59 @@ +Number of intervals: 626 +Longest interval was: 114748301 +Total length of covered territory: 2832598113 +Theoretical max subset length: 56651962 +Processing... + 1. Batch of 10 | 29268124 |close-out | 11 | So far 29268124 | Remains 2803329989 + 2. Batch of 1 | 73835823 |godzilla | 11 | So far 103103947 | Remains 2729494166 + 3. Batch of 40 | 22774904 |normal | 52 | So far 125878851 | Remains 2706719262 + 4. Batch of 2 | 56672574 |normal | 54 | So far 182551425 | Remains 2650046688 + 5. Batch of 8 | 63461505 |normal | 62 | So far 246012930 | Remains 2586585183 + 6. Batch of 20 | 69675187 |normal | 82 | So far 315688117 | Remains 2516909996 + 7. Batch of 7 | 54110622 |close-out | 89 | So far 369798739 | Remains 2462799374 + 8. Batch of 1 | 84213158 |godzilla | 89 | So far 454011897 | Remains 2378586216 + 9. Batch of 8 | 18867510 |normal | 98 | So far 472879407 | Remains 2359718706 + 10. Batch of 11 | 65958202 |normal | 109 | So far 538837609 | Remains 2293760504 + 11. Batch of 1 | 14505967 |close-out | 110 | So far 553343576 | Remains 2279254537 + 12. Batch of 1 | 100537106 |godzilla | 110 | So far 653880682 | Remains 2178717431 + 13. Batch of 20 | 60255306 |normal | 131 | So far 714135988 | Remains 2118462125 + 14. Batch of 1 | 15638045 |close-out | 132 | So far 729774033 | Remains 2102824080 + 15. Batch of 1 | 114748301 |godzilla | 132 | So far 844522334 | Remains 1988075779 + 16. Batch of 5 | 47153331 |normal | 138 | So far 891675665 | Remains 1940922448 + 17. Batch of 1 | 42230486 |normal | 139 | So far 933906151 | Remains 1898691962 + 18. Batch of 2 | 63402597 |normal | 141 | So far 997308748 | Remains 1835289365 + 19. Batch of 29 | 58275902 |normal | 170 | So far 1055584650 | Remains 1777013463 + 20. Batch of 26 | 59425399 |close-out | 196 | So far 1115010049 | Remains 1717588064 + 21. Batch of 1 | 61728923 |godzilla | 196 | So far 1176738972 | Remains 1655859141 + 22. Batch of 7 | 70811404 |normal | 204 | So far 1247550376 | Remains 1585047737 + 23. Batch of 45 | 68890667 |normal | 249 | So far 1316441043 | Remains 1516157070 + 24. Batch of 48 | 40724559 |normal | 297 | So far 1357165602 | Remains 1475432511 + 25. Batch of 6 | 32653926 |normal | 303 | So far 1389819528 | Remains 1442778585 + 26. Batch of 1 | 38440851 |normal | 304 | So far 1428260379 | Remains 1404337734 + 27. Batch of 3 | 59487568 |normal | 307 | So far 1487747947 | Remains 1344850166 + 28. Batch of 52 | 50107468 |normal | 359 | So far 1537855415 | Remains 1294742698 + 29. Batch of 6 | 69877957 |normal | 365 | So far 1607733372 | Remains 1224864741 + 30. Batch of 61 | 47109734 |close-out | 426 | So far 1654843106 | Remains 1177755007 + 31. Batch of 1 | 74420626 |godzilla | 426 | So far 1729263732 | Remains 1103334381 + 32. Batch of 7 | 60542497 |normal | 434 | So far 1789806229 | Remains 1042791884 + 33. Batch of 4 | 41443375 |normal | 438 | So far 1831249604 | Remains 1001348509 + 34. Batch of 3 | 45648805 |normal | 441 | So far 1876898409 | Remains 955699704 + 35. Batch of 1 | 27616817 |close-out | 442 | So far 1904515226 | Remains 928082887 + 36. Batch of 1 | 71516775 |godzilla | 442 | So far 1976032001 | Remains 856566112 + 37. Batch of 6 | 68861229 |normal | 449 | So far 2044893230 | Remains 787704883 + 38. Batch of 5 | 51020696 |close-out | 454 | So far 2095913926 | Remains 736684187 + 39. Batch of 1 | 88349539 |godzilla | 454 | So far 2184263465 | Remains 648334648 + 40. Batch of 8 | 64207842 |normal | 463 | So far 2248471307 | Remains 584126806 + 41. Batch of 30 | 52347234 |normal | 493 | So far 2300818541 | Remains 531779572 + 42. Batch of 33 | 65660090 |normal | 526 | So far 2366478631 | Remains 466119482 + 43. Batch of 5 | 55653364 |normal | 531 | So far 2422131995 | Remains 410466118 + 44. Batch of 3 | 69023350 |normal | 534 | So far 2491155345 | Remains 341442768 + 45. Batch of 7 | 61512871 |normal | 541 | So far 2552668216 | Remains 279929897 + 46. Batch of 55 | 60175036 |normal | 596 | So far 2612843252 | Remains 219754861 + 47. Batch of 15 | 70402555 |normal | 611 | So far 2683245807 | Remains 149352306 + 48. Batch of 7 | 56163767 |normal | 618 | So far 2739409574 | Remains 93188539 + 49. Batch of 4 | 58181219 |normal | 622 | So far 2797590793 | Remains 35007320 + 50. Batch of 5 | 35007320 |finalize | 626 | So far 2832598113 | Remains 0 +Done. +Grouped intervals into 50 batches. +Wrote 50 interval files to "output_intervals/n_of_N/scattered.interval_list" +Wrote a JSON stub to "scattered_intervals.json" \ No newline at end of file diff --git a/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/10_of_50/scattered.interval_list b/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/10_of_50/scattered.interval_list new file mode 100644 index 0000000..089ec7b --- /dev/null +++ b/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/10_of_50/scattered.interval_list @@ -0,0 +1,100 @@ +@HD VN:1.4 SO:coordinate +@SQ SN:1 LN:249250621 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Homo Sapiens +@SQ SN:2 LN:243199373 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta 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M5:3238fb74ea87ae857f9c7508d315babb SP:Homo Sapiens +@SQ SN:GL000209.1 LN:159169 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:f40598e2a5a6b26e84a3775e0d1e2c81 SP:Homo Sapiens +@SQ SN:GL000218.1 LN:161147 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1d708b54644c26c7e01c2dad5426d38c SP:Homo Sapiens +@SQ SN:GL000220.1 LN:161802 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:fc35de963c57bf7648429e6454f1c9db SP:Homo Sapiens +@SQ SN:GL000213.1 LN:164239 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:9d424fdcc98866650b58f004080a992a SP:Homo Sapiens +@SQ SN:GL000211.1 LN:166566 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:7daaa45c66b288847b9b32b964e623d3 SP:Homo Sapiens +@SQ SN:GL000199.1 LN:169874 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M5:f977edd13bac459cb2ed4a5457dba1b3 SP:Homo Sapiens +@SQ SN:GL000224.1 LN:179693 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:d5b2fc04f6b41b212a4198a07f450e20 SP:Homo Sapiens +@SQ SN:GL000223.1 LN:180455 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:399dfa03bf32022ab52a846f7ca35b30 SP:Homo Sapiens +@SQ SN:GL000195.1 LN:182896 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:5d9ec007868d517e73543b005ba48535 SP:Homo Sapiens +@SQ SN:GL000212.1 LN:186858 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:563531689f3dbd691331fd6c5730a88b SP:Homo Sapiens +@SQ SN:GL000222.1 LN:186861 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6fe9abac455169f50470f5a6b01d0f59 SP:Homo Sapiens +@SQ SN:GL000200.1 LN:187035 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:75e4c8d17cd4addf3917d1703cacaf25 SP:Homo Sapiens +@SQ SN:GL000193.1 LN:189789 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:dbb6e8ece0b5de29da56601613007c2a SP:Homo Sapiens +@SQ SN:GL000194.1 LN:191469 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6ac8f815bf8e845bb3031b73f812c012 SP:Homo Sapiens +@SQ SN:GL000225.1 LN:211173 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:63945c3e6962f28ffd469719a747e73c SP:Homo Sapiens +@SQ SN:GL000192.1 LN:547496 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:325ba9e808f669dfeee210fdd7b470ac SP:Homo Sapiens +@SQ SN:NC_007605 LN:171823 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:NC_007605.1 M5:6743bd63b3ff2b5b8985d8933c53290a SP:Epstein-Barr virus +@PG ID:1 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[N.regions.interval_list, expensive.parsed.interval_list] OUTPUT=joined.regions.interval_list ACTION=UNION PADDING=0 UNIQUE=false SORT=true HEAD=1 SCATTER_COUNT=1 INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@PG ID:2 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[joined.regions.interval_list, exome.evaluation.padded.interval_list] OUTPUT=whole.genome.calling.region.interval_list ACTION=SUBTRACT HEAD=1 INVERT=true PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@CO demo intervals scattered 50-ways +4 190203582 190540581 + interval-133 +4 190566582 190567581 + interval-134 +4 190684582 191154276 + interval-135 +5 10001 17530657 + interval-136 +5 17580658 46405641 + interval-137 diff --git a/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/17_of_50/scattered.interval_list b/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/17_of_50/scattered.interval_list new file mode 100644 index 0000000..654ae39 --- /dev/null +++ b/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/17_of_50/scattered.interval_list @@ -0,0 +1,90 @@ +@HD VN:1.4 SO:coordinate +@SQ SN:1 LN:249250621 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Homo Sapiens +@SQ SN:2 LN:243199373 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:a0d9851da00400dec1098a9255ac712e SP:Homo Sapiens +@SQ SN:3 LN:198022430 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:fdfd811849cc2fadebc929bb925902e5 SP:Homo Sapiens +@SQ SN:4 LN:191154276 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:23dccd106897542ad87d2765d28a19a1 SP:Homo Sapiens +@SQ SN:5 LN:180915260 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:0740173db9ffd264d728f32784845cd7 SP:Homo Sapiens +@SQ SN:6 LN:171115067 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1d3a93a248d92a729ee764823acbbc6b SP:Homo Sapiens +@SQ SN:7 LN:159138663 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:618366e953d6aaad97dbe4777c29375e SP:Homo Sapiens +@SQ SN:8 LN:146364022 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:96f514a9929e410c6651697bded59aec SP:Homo Sapiens +@SQ SN:9 LN:141213431 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:3e273117f15e0a400f01055d9f393768 SP:Homo Sapiens +@SQ SN:10 LN:135534747 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:988c28e000e84c26d552359af1ea2e1d SP:Homo Sapiens +@SQ SN:11 LN:135006516 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:98c59049a2df285c76ffb1c6db8f8b96 SP:Homo Sapiens +@SQ SN:12 LN:133851895 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:51851ac0e1a115847ad36449b0015864 SP:Homo Sapiens +@SQ SN:13 LN:115169878 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:283f8d7892baa81b510a015719ca7b0b SP:Homo Sapiens +@SQ SN:14 LN:107349540 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:98f3cae32b2a2e9524bc19813927542e SP:Homo Sapiens +@SQ SN:15 LN:102531392 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:e5645a794a8238215b2cd77acb95a078 SP:Homo Sapiens +@SQ SN:16 LN:90354753 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:fc9b1a7b42b97a864f56b348b06095e6 SP:Homo Sapiens +@SQ SN:17 LN:81195210 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:351f64d4f4f9ddd45b35336ad97aa6de SP:Homo Sapiens +@SQ SN:18 LN:78077248 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c SP:Homo Sapiens +@SQ SN:19 LN:59128983 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1aacd71f30db8e561810913e0b72636d SP:Homo Sapiens +@SQ SN:20 LN:63025520 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:0dec9660ec1efaaf33281c0d5ea2560f SP:Homo Sapiens +@SQ SN:21 LN:48129895 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:2979a6085bfe28e3ad6f552f361ed74d SP:Homo Sapiens +@SQ SN:22 LN:51304566 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:a718acaa6135fdca8357d5bfe94211dd SP:Homo Sapiens +@SQ SN:X LN:155270560 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:7e0e2e580297b7764e31dbc80c2540dd SP:Homo Sapiens +@SQ SN:Y LN:59373566 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1fa3474750af0948bdf97d5a0ee52e51 SP:Homo Sapiens +@SQ SN:MT LN:16569 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:c68f52674c9fb33aef52dcf399755519 SP:Homo Sapiens +@SQ SN:GL000207.1 LN:4262 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:f3814841f1939d3ca19072d9e89f3fd7 SP:Homo Sapiens +@SQ SN:GL000226.1 LN:15008 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1c1b2cd1fccbc0a99b6a447fa24d1504 SP:Homo Sapiens +@SQ SN:GL000229.1 LN:19913 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:d0f40ec87de311d8e715b52e4c7062e1 SP:Homo Sapiens +@SQ SN:GL000231.1 LN:27386 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:ba8882ce3a1efa2080e5d29b956568a4 SP:Homo Sapiens +@SQ SN:GL000210.1 LN:27682 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:851106a74238044126131ce2a8e5847c SP:Homo Sapiens +@SQ SN:GL000239.1 LN:33824 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:99795f15702caec4fa1c4e15f8a29c07 SP:Homo Sapiens +@SQ SN:GL000235.1 LN:34474 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:118a25ca210cfbcdfb6c2ebb249f9680 SP:Homo Sapiens +@SQ SN:GL000201.1 LN:36148 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:dfb7e7ec60ffdcb85cb359ea28454ee9 SP:Homo Sapiens +@SQ SN:GL000247.1 LN:36422 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:7de00226bb7df1c57276ca6baabafd15 SP:Homo Sapiens +@SQ SN:GL000245.1 LN:36651 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:89bc61960f37d94abf0df2d481ada0ec SP:Homo Sapiens +@SQ SN:GL000197.1 LN:37175 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6f5efdd36643a9b8c8ccad6f2f1edc7b SP:Homo Sapiens +@SQ SN:GL000203.1 LN:37498 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:96358c325fe0e70bee73436e8bb14dbd SP:Homo Sapiens +@SQ SN:GL000246.1 LN:38154 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:e4afcd31912af9d9c2546acf1cb23af2 SP:Homo Sapiens +@SQ SN:GL000249.1 LN:38502 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1d78abec37c15fe29a275eb08d5af236 SP:Homo Sapiens +@SQ SN:GL000196.1 LN:38914 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:d92206d1bb4c3b4019c43c0875c06dc0 SP:Homo Sapiens +@SQ SN:GL000248.1 LN:39786 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:5a8e43bec9be36c7b49c84d585107776 SP:Homo Sapiens +@SQ SN:GL000244.1 LN:39929 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:0996b4475f353ca98bacb756ac479140 SP:Homo Sapiens +@SQ SN:GL000238.1 LN:39939 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:131b1efc3270cc838686b54e7c34b17b SP:Homo Sapiens +@SQ SN:GL000202.1 LN:40103 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:06cbf126247d89664a4faebad130fe9c SP:Homo Sapiens +@SQ SN:GL000234.1 LN:40531 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:93f998536b61a56fd0ff47322a911d4b SP:Homo Sapiens +@SQ SN:GL000232.1 LN:40652 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:3e06b6741061ad93a8587531307057d8 SP:Homo Sapiens +@SQ SN:GL000206.1 LN:41001 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:43f69e423533e948bfae5ce1d45bd3f1 SP:Homo Sapiens +@SQ SN:GL000240.1 LN:41933 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:445a86173da9f237d7bcf41c6cb8cc62 SP:Homo Sapiens +@SQ SN:GL000236.1 LN:41934 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:fdcd739913efa1fdc64b6c0cd7016779 SP:Homo Sapiens +@SQ SN:GL000241.1 LN:42152 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:ef4258cdc5a45c206cea8fc3e1d858cf SP:Homo Sapiens +@SQ SN:GL000243.1 LN:43341 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:cc34279a7e353136741c9fce79bc4396 SP:Homo Sapiens +@SQ SN:GL000242.1 LN:43523 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:2f8694fc47576bc81b5fe9e7de0ba49e SP:Homo Sapiens +@SQ SN:GL000230.1 LN:43691 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:b4eb71ee878d3706246b7c1dbef69299 SP:Homo Sapiens +@SQ SN:GL000237.1 LN:45867 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:e0c82e7751df73f4f6d0ed30cdc853c0 SP:Homo Sapiens +@SQ SN:GL000233.1 LN:45941 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:7fed60298a8d62ff808b74b6ce820001 SP:Homo Sapiens +@SQ SN:GL000204.1 LN:81310 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:efc49c871536fa8d79cb0a06fa739722 SP:Homo Sapiens +@SQ SN:GL000198.1 LN:90085 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:868e7784040da90d900d2d1b667a1383 SP:Homo Sapiens +@SQ SN:GL000208.1 LN:92689 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:aa81be49bf3fe63a79bdc6a6f279abf6 SP:Homo Sapiens +@SQ SN:GL000191.1 LN:106433 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:d75b436f50a8214ee9c2a51d30b2c2cc SP:Homo Sapiens +@SQ SN:GL000227.1 LN:128374 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:a4aead23f8053f2655e468bcc6ecdceb SP:Homo Sapiens +@SQ SN:GL000228.1 LN:129120 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:c5a17c97e2c1a0b6a9cc5a6b064b714f SP:Homo Sapiens +@SQ SN:GL000214.1 LN:137718 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:46c2032c37f2ed899eb41c0473319a69 SP:Homo Sapiens +@SQ SN:GL000221.1 LN:155397 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:3238fb74ea87ae857f9c7508d315babb SP:Homo Sapiens +@SQ SN:GL000209.1 LN:159169 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:f40598e2a5a6b26e84a3775e0d1e2c81 SP:Homo Sapiens +@SQ SN:GL000218.1 LN:161147 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1d708b54644c26c7e01c2dad5426d38c SP:Homo Sapiens +@SQ SN:GL000220.1 LN:161802 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:fc35de963c57bf7648429e6454f1c9db SP:Homo Sapiens +@SQ SN:GL000213.1 LN:164239 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:9d424fdcc98866650b58f004080a992a SP:Homo Sapiens +@SQ SN:GL000211.1 LN:166566 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:7daaa45c66b288847b9b32b964e623d3 SP:Homo Sapiens +@SQ SN:GL000199.1 LN:169874 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:569af3b73522fab4b40995ae4944e78e SP:Homo Sapiens +@SQ SN:GL000217.1 LN:172149 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6d243e18dea1945fb7f2517615b8f52e SP:Homo Sapiens +@SQ SN:GL000216.1 LN:172294 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:642a232d91c486ac339263820aef7fe0 SP:Homo Sapiens +@SQ SN:GL000215.1 LN:172545 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:5eb3b418480ae67a997957c909375a73 SP:Homo Sapiens +@SQ SN:GL000205.1 LN:174588 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:d22441398d99caf673e9afb9a1908ec5 SP:Homo Sapiens +@SQ SN:GL000219.1 LN:179198 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:f977edd13bac459cb2ed4a5457dba1b3 SP:Homo Sapiens +@SQ SN:GL000224.1 LN:179693 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:d5b2fc04f6b41b212a4198a07f450e20 SP:Homo Sapiens +@SQ SN:GL000223.1 LN:180455 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:399dfa03bf32022ab52a846f7ca35b30 SP:Homo Sapiens +@SQ SN:GL000195.1 LN:182896 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:5d9ec007868d517e73543b005ba48535 SP:Homo Sapiens +@SQ SN:GL000212.1 LN:186858 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:563531689f3dbd691331fd6c5730a88b SP:Homo Sapiens +@SQ SN:GL000222.1 LN:186861 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6fe9abac455169f50470f5a6b01d0f59 SP:Homo Sapiens +@SQ SN:GL000200.1 LN:187035 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:75e4c8d17cd4addf3917d1703cacaf25 SP:Homo Sapiens +@SQ SN:GL000193.1 LN:189789 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:dbb6e8ece0b5de29da56601613007c2a SP:Homo Sapiens +@SQ SN:GL000194.1 LN:191469 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6ac8f815bf8e845bb3031b73f812c012 SP:Homo Sapiens +@SQ SN:GL000225.1 LN:211173 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:63945c3e6962f28ffd469719a747e73c SP:Homo Sapiens +@SQ SN:GL000192.1 LN:547496 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:325ba9e808f669dfeee210fdd7b470ac SP:Homo Sapiens +@SQ SN:NC_007605 LN:171823 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:NC_007605.1 M5:6743bd63b3ff2b5b8985d8933c53290a SP:Epstein-Barr virus +@PG ID:1 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[N.regions.interval_list, expensive.parsed.interval_list] OUTPUT=joined.regions.interval_list ACTION=UNION PADDING=0 UNIQUE=false SORT=true HEAD=1 SCATTER_COUNT=1 INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@PG ID:2 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[joined.regions.interval_list, exome.evaluation.padded.interval_list] OUTPUT=whole.genome.calling.region.interval_list ACTION=SUBTRACT HEAD=1 INVERT=true PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@CO demo intervals scattered 50-ways +5 49405642 91636128 + interval-138 diff --git a/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/18_of_50/scattered.interval_list b/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/18_of_50/scattered.interval_list new file mode 100644 index 0000000..3723228 --- /dev/null +++ b/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/18_of_50/scattered.interval_list @@ -0,0 +1,91 @@ +@HD VN:1.4 SO:coordinate +@SQ SN:1 LN:249250621 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Homo Sapiens +@SQ SN:2 LN:243199373 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:a0d9851da00400dec1098a9255ac712e SP:Homo Sapiens +@SQ SN:3 LN:198022430 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:fdfd811849cc2fadebc929bb925902e5 SP:Homo Sapiens +@SQ SN:4 LN:191154276 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:23dccd106897542ad87d2765d28a19a1 SP:Homo Sapiens +@SQ SN:5 LN:180915260 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta 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M5:a718acaa6135fdca8357d5bfe94211dd SP:Homo Sapiens +@SQ SN:X LN:155270560 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:7e0e2e580297b7764e31dbc80c2540dd SP:Homo Sapiens +@SQ SN:Y LN:59373566 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1fa3474750af0948bdf97d5a0ee52e51 SP:Homo Sapiens +@SQ SN:MT LN:16569 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:c68f52674c9fb33aef52dcf399755519 SP:Homo Sapiens +@SQ SN:GL000207.1 LN:4262 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:f3814841f1939d3ca19072d9e89f3fd7 SP:Homo Sapiens +@SQ SN:GL000226.1 LN:15008 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1c1b2cd1fccbc0a99b6a447fa24d1504 SP:Homo Sapiens +@SQ SN:GL000229.1 LN:19913 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UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:ef4258cdc5a45c206cea8fc3e1d858cf SP:Homo Sapiens +@SQ SN:GL000243.1 LN:43341 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:cc34279a7e353136741c9fce79bc4396 SP:Homo Sapiens +@SQ SN:GL000242.1 LN:43523 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:2f8694fc47576bc81b5fe9e7de0ba49e SP:Homo Sapiens +@SQ SN:GL000230.1 LN:43691 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:b4eb71ee878d3706246b7c1dbef69299 SP:Homo Sapiens +@SQ SN:GL000237.1 LN:45867 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:e0c82e7751df73f4f6d0ed30cdc853c0 SP:Homo Sapiens +@SQ SN:GL000233.1 LN:45941 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 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M5:fc35de963c57bf7648429e6454f1c9db SP:Homo Sapiens +@SQ SN:GL000213.1 LN:164239 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:9d424fdcc98866650b58f004080a992a SP:Homo Sapiens +@SQ SN:GL000211.1 LN:166566 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:7daaa45c66b288847b9b32b964e623d3 SP:Homo Sapiens +@SQ SN:GL000199.1 LN:169874 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:569af3b73522fab4b40995ae4944e78e SP:Homo Sapiens +@SQ SN:GL000217.1 LN:172149 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6d243e18dea1945fb7f2517615b8f52e SP:Homo Sapiens +@SQ SN:GL000216.1 LN:172294 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:642a232d91c486ac339263820aef7fe0 SP:Homo Sapiens +@SQ SN:GL000215.1 LN:172545 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:5eb3b418480ae67a997957c909375a73 SP:Homo Sapiens +@SQ SN:GL000205.1 LN:174588 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:d22441398d99caf673e9afb9a1908ec5 SP:Homo Sapiens +@SQ SN:GL000219.1 LN:179198 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:f977edd13bac459cb2ed4a5457dba1b3 SP:Homo Sapiens +@SQ SN:GL000224.1 LN:179693 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:d5b2fc04f6b41b212a4198a07f450e20 SP:Homo Sapiens +@SQ SN:GL000223.1 LN:180455 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:399dfa03bf32022ab52a846f7ca35b30 SP:Homo Sapiens +@SQ SN:GL000195.1 LN:182896 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 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UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:dbb6e8ece0b5de29da56601613007c2a SP:Homo Sapiens +@SQ SN:GL000194.1 LN:191469 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6ac8f815bf8e845bb3031b73f812c012 SP:Homo Sapiens +@SQ SN:GL000225.1 LN:211173 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:63945c3e6962f28ffd469719a747e73c SP:Homo Sapiens +@SQ SN:GL000192.1 LN:547496 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:325ba9e808f669dfeee210fdd7b470ac SP:Homo Sapiens +@SQ SN:NC_007605 LN:171823 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:NC_007605.1 M5:6743bd63b3ff2b5b8985d8933c53290a SP:Epstein-Barr virus +@PG ID:1 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[N.regions.interval_list, expensive.parsed.interval_list] OUTPUT=joined.regions.interval_list ACTION=UNION PADDING=0 UNIQUE=false SORT=true HEAD=1 SCATTER_COUNT=1 INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@PG ID:2 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[joined.regions.interval_list, exome.evaluation.padded.interval_list] OUTPUT=whole.genome.calling.region.interval_list ACTION=SUBTRACT HEAD=1 INVERT=true PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@CO demo intervals scattered 50-ways +1 10001 177417 + interval-1 +1 227418 267719 + interval-2 +1 317720 471368 + interval-3 +1 521369 2634220 + interval-4 +1 2684221 3845268 + interval-5 +1 3995269 13053050 + interval-6 +1 13102999 13219912 + interval-7 +1 13319913 13557162 + interval-8 +1 13607163 17125658 + 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M5:dbb6e8ece0b5de29da56601613007c2a SP:Homo Sapiens +@SQ SN:GL000194.1 LN:191469 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6ac8f815bf8e845bb3031b73f812c012 SP:Homo Sapiens +@SQ SN:GL000225.1 LN:211173 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:63945c3e6962f28ffd469719a747e73c SP:Homo Sapiens +@SQ SN:GL000192.1 LN:547496 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:325ba9e808f669dfeee210fdd7b470ac SP:Homo Sapiens +@SQ SN:NC_007605 LN:171823 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:NC_007605.1 M5:6743bd63b3ff2b5b8985d8933c53290a SP:Epstein-Barr virus +@PG ID:1 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[N.regions.interval_list, expensive.parsed.interval_list] OUTPUT=joined.regions.interval_list ACTION=UNION PADDING=0 UNIQUE=false SORT=true HEAD=1 SCATTER_COUNT=1 INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@PG ID:2 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[joined.regions.interval_list, exome.evaluation.padded.interval_list] OUTPUT=whole.genome.calling.region.interval_list ACTION=SUBTRACT HEAD=1 INVERT=true PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@CO demo intervals scattered 50-ways +6 32697156 57206155 + interval-170 +6 57223156 57224155 + interval-171 +6 57236156 57239155 + interval-172 +6 57244647 57244846 + interval-173 +6 57246777 57247048 + interval-174 +6 57267156 57279155 + interval-175 +6 57285156 57289155 + interval-176 +6 57298156 57302155 + interval-177 +6 57317156 57322155 + interval-178 +6 57372236 57372407 + interval-179 +6 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UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:dbb6e8ece0b5de29da56601613007c2a SP:Homo Sapiens +@SQ SN:GL000194.1 LN:191469 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6ac8f815bf8e845bb3031b73f812c012 SP:Homo Sapiens +@SQ SN:GL000225.1 LN:211173 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:63945c3e6962f28ffd469719a747e73c SP:Homo Sapiens +@SQ SN:GL000192.1 LN:547496 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:325ba9e808f669dfeee210fdd7b470ac SP:Homo Sapiens +@SQ SN:NC_007605 LN:171823 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:NC_007605.1 M5:6743bd63b3ff2b5b8985d8933c53290a SP:Epstein-Barr virus +@PG ID:1 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[N.regions.interval_list, expensive.parsed.interval_list] 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OUTPUT=joined.regions.interval_list ACTION=UNION PADDING=0 UNIQUE=false SORT=true HEAD=1 SCATTER_COUNT=1 INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@PG ID:2 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[joined.regions.interval_list, exome.evaluation.padded.interval_list] OUTPUT=whole.genome.calling.region.interval_list ACTION=SUBTRACT HEAD=1 INVERT=true PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@CO demo intervals scattered 50-ways +8 86726452 142766515 + interval-304 +8 142816516 145332588 + interval-305 +8 145432589 146364022 + interval-306 diff --git a/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/28_of_50/scattered.interval_list 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PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[joined.regions.interval_list, exome.evaluation.padded.interval_list] OUTPUT=whole.genome.calling.region.interval_list ACTION=SUBTRACT HEAD=1 INVERT=true PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@CO demo intervals scattered 50-ways +9 10001 39663686 + interval-307 +9 39713687 39974796 + interval-308 +9 40024797 40233029 + interval-309 +9 40283030 40425834 + interval-310 +9 40475835 40940341 + interval-311 +9 40990342 41143214 + interval-312 +9 41193215 41365793 + interval-313 +9 41415794 42613955 + interval-314 +9 42663956 43213698 + interval-315 +9 43313699 43946569 + interval-316 +9 43996570 44676646 + interval-317 +9 44726647 44908293 + interval-318 +9 44958294 45250203 + interval-319 +9 45350204 45815521 + interval-320 +9 45865522 46216430 + interval-321 +9 46266431 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M5:6743bd63b3ff2b5b8985d8933c53290a SP:Epstein-Barr virus +@PG ID:1 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[N.regions.interval_list, expensive.parsed.interval_list] OUTPUT=joined.regions.interval_list ACTION=UNION PADDING=0 UNIQUE=false SORT=true HEAD=1 SCATTER_COUNT=1 INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@PG ID:2 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[joined.regions.interval_list, exome.evaluation.padded.interval_list] OUTPUT=whole.genome.calling.region.interval_list ACTION=SUBTRACT HEAD=1 INVERT=true PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@CO demo intervals scattered 50-ways +9 70835469 92343416 + interval-359 +9 92443417 92528796 + interval-360 +9 92678797 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UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:dbb6e8ece0b5de29da56601613007c2a SP:Homo Sapiens +@SQ SN:GL000194.1 LN:191469 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6ac8f815bf8e845bb3031b73f812c012 SP:Homo Sapiens +@SQ SN:GL000225.1 LN:211173 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:63945c3e6962f28ffd469719a747e73c SP:Homo Sapiens +@SQ SN:GL000192.1 LN:547496 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:325ba9e808f669dfeee210fdd7b470ac SP:Homo Sapiens +@SQ SN:NC_007605 LN:171823 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:NC_007605.1 M5:6743bd63b3ff2b5b8985d8933c53290a SP:Epstein-Barr virus +@PG ID:1 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[N.regions.interval_list, expensive.parsed.interval_list] 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UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:dbb6e8ece0b5de29da56601613007c2a SP:Homo Sapiens +@SQ SN:GL000194.1 LN:191469 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6ac8f815bf8e845bb3031b73f812c012 SP:Homo Sapiens +@SQ SN:GL000225.1 LN:211173 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:63945c3e6962f28ffd469719a747e73c SP:Homo Sapiens +@SQ SN:GL000192.1 LN:547496 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:325ba9e808f669dfeee210fdd7b470ac SP:Homo Sapiens +@SQ SN:NC_007605 LN:171823 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:NC_007605.1 M5:6743bd63b3ff2b5b8985d8933c53290a SP:Epstein-Barr virus +@PG ID:1 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[N.regions.interval_list, expensive.parsed.interval_list] 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PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[joined.regions.interval_list, exome.evaluation.padded.interval_list] OUTPUT=whole.genome.calling.region.interval_list ACTION=SUBTRACT HEAD=1 INVERT=true PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@CO demo intervals scattered 50-ways +11 96437585 135006516 + interval-438 +12 60001 95739 + interval-439 +12 145740 7189876 + interval-440 diff --git a/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/35_of_50/scattered.interval_list b/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/35_of_50/scattered.interval_list new file mode 100644 index 0000000..d462c2f --- /dev/null +++ b/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/35_of_50/scattered.interval_list @@ -0,0 +1,90 @@ +@HD VN:1.4 SO:coordinate 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M5:6743bd63b3ff2b5b8985d8933c53290a SP:Epstein-Barr virus +@PG ID:1 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[N.regions.interval_list, expensive.parsed.interval_list] OUTPUT=joined.regions.interval_list ACTION=UNION PADDING=0 UNIQUE=false SORT=true HEAD=1 SCATTER_COUNT=1 INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@PG ID:2 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[joined.regions.interval_list, exome.evaluation.padded.interval_list] OUTPUT=whole.genome.calling.region.interval_list ACTION=SUBTRACT HEAD=1 INVERT=true PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@CO demo intervals scattered 50-ways +12 37856695 109373470 + interval-442 diff --git 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SCATTER_COUNT=1 INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@PG ID:2 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[joined.regions.interval_list, exome.evaluation.padded.interval_list] OUTPUT=whole.genome.calling.region.interval_list ACTION=SUBTRACT HEAD=1 INVERT=true PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@CO demo intervals scattered 50-ways +12 109423471 121965036 + interval-443 +12 121965237 122530623 + interval-444 +12 122580624 123928080 + interval-445 +12 123928281 132706992 + interval-446 +12 132806993 133851895 + interval-447 +13 19020001 63603210 + interval-448 diff --git a/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/38_of_50/scattered.interval_list 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CL:net.sf.picard.util.IntervalListTools INPUT=[N.regions.interval_list, expensive.parsed.interval_list] OUTPUT=joined.regions.interval_list ACTION=UNION PADDING=0 UNIQUE=false SORT=true HEAD=1 SCATTER_COUNT=1 INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@PG ID:2 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[joined.regions.interval_list, exome.evaluation.padded.interval_list] OUTPUT=whole.genome.calling.region.interval_list ACTION=SUBTRACT HEAD=1 INVERT=true PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@CO demo intervals scattered 50-ways +16 46497427 88389383 + interval-493 +16 88439384 90354753 + interval-494 +17 1 296626 + interval-495 +17 396627 20767841 + interval-496 +17 20768675 20768876 + interval-497 +17 20769808 20770070 + interval-498 +17 20784842 21196841 + interval-499 +17 21198935 21199133 + interval-500 +17 21199346 21199538 + interval-501 +17 21201608 21201845 + interval-502 +17 21202137 21202292 + interval-503 +17 21203804 21204024 + interval-504 +17 21204133 21204359 + interval-505 +17 21205402 21205625 + interval-506 +17 21206442 21206600 + interval-507 +17 21207685 21207919 + interval-508 +17 21208310 21208494 + interval-509 +17 21215401 21215647 + interval-510 +17 21216751 21217123 + interval-511 +17 21217406 21217596 + interval-512 +17 21254842 21298841 + interval-513 +17 21299842 21302841 + interval-514 +17 21318602 21320010 + interval-515 +17 21321842 21322841 + interval-516 +17 21353842 21506841 + interval-517 +17 21666609 21667841 + interval-518 +17 21670842 21895841 + interval-519 +17 21896842 21902841 + interval-520 +17 21907842 22207841 + interval-521 +17 22211842 22244841 + interval-522 +17 22262842 22263006 + interval-523 +17 25263007 25263841 + interval-524 +17 25338842 25339841 + interval-525 diff --git a/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/43_of_50/scattered.interval_list b/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/43_of_50/scattered.interval_list new file mode 100644 index 0000000..eafd99a --- /dev/null +++ b/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/43_of_50/scattered.interval_list @@ -0,0 +1,94 @@ +@HD VN:1.4 SO:coordinate +@SQ SN:1 LN:249250621 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Homo Sapiens +@SQ SN:2 LN:243199373 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:a0d9851da00400dec1098a9255ac712e SP:Homo Sapiens +@SQ SN:3 LN:198022430 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:fdfd811849cc2fadebc929bb925902e5 SP:Homo Sapiens +@SQ SN:4 LN:191154276 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:23dccd106897542ad87d2765d28a19a1 SP:Homo Sapiens +@SQ SN:5 LN:180915260 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:0740173db9ffd264d728f32784845cd7 SP:Homo Sapiens +@SQ SN:6 LN:171115067 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1d3a93a248d92a729ee764823acbbc6b SP:Homo Sapiens +@SQ SN:7 LN:159138663 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:618366e953d6aaad97dbe4777c29375e SP:Homo Sapiens +@SQ SN:8 LN:146364022 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:96f514a9929e410c6651697bded59aec SP:Homo Sapiens +@SQ SN:9 LN:141213431 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:3e273117f15e0a400f01055d9f393768 SP:Homo Sapiens +@SQ SN:10 LN:135534747 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:988c28e000e84c26d552359af1ea2e1d SP:Homo Sapiens +@SQ SN:11 LN:135006516 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:98c59049a2df285c76ffb1c6db8f8b96 SP:Homo Sapiens +@SQ SN:12 LN:133851895 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:51851ac0e1a115847ad36449b0015864 SP:Homo Sapiens +@SQ SN:13 LN:115169878 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:283f8d7892baa81b510a015719ca7b0b SP:Homo Sapiens +@SQ SN:14 LN:107349540 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:98f3cae32b2a2e9524bc19813927542e SP:Homo Sapiens +@SQ SN:15 LN:102531392 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:e5645a794a8238215b2cd77acb95a078 SP:Homo Sapiens +@SQ SN:16 LN:90354753 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:fc9b1a7b42b97a864f56b348b06095e6 SP:Homo Sapiens +@SQ SN:17 LN:81195210 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:351f64d4f4f9ddd45b35336ad97aa6de SP:Homo Sapiens +@SQ SN:18 LN:78077248 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:b15d4b2d29dde9d3e4f93d1d0f2cbc9c SP:Homo Sapiens +@SQ SN:19 LN:59128983 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1aacd71f30db8e561810913e0b72636d SP:Homo Sapiens +@SQ SN:20 LN:63025520 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:0dec9660ec1efaaf33281c0d5ea2560f SP:Homo Sapiens +@SQ SN:21 LN:48129895 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:2979a6085bfe28e3ad6f552f361ed74d SP:Homo Sapiens +@SQ SN:22 LN:51304566 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:a718acaa6135fdca8357d5bfe94211dd SP:Homo Sapiens +@SQ SN:X LN:155270560 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:7e0e2e580297b7764e31dbc80c2540dd SP:Homo Sapiens +@SQ SN:Y LN:59373566 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1fa3474750af0948bdf97d5a0ee52e51 SP:Homo Sapiens +@SQ SN:MT LN:16569 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:c68f52674c9fb33aef52dcf399755519 SP:Homo Sapiens +@SQ SN:GL000207.1 LN:4262 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:f3814841f1939d3ca19072d9e89f3fd7 SP:Homo Sapiens +@SQ SN:GL000226.1 LN:15008 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1c1b2cd1fccbc0a99b6a447fa24d1504 SP:Homo Sapiens +@SQ SN:GL000229.1 LN:19913 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:d0f40ec87de311d8e715b52e4c7062e1 SP:Homo Sapiens +@SQ SN:GL000231.1 LN:27386 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:ba8882ce3a1efa2080e5d29b956568a4 SP:Homo Sapiens +@SQ SN:GL000210.1 LN:27682 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:851106a74238044126131ce2a8e5847c SP:Homo Sapiens +@SQ SN:GL000239.1 LN:33824 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:99795f15702caec4fa1c4e15f8a29c07 SP:Homo Sapiens +@SQ SN:GL000235.1 LN:34474 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:118a25ca210cfbcdfb6c2ebb249f9680 SP:Homo Sapiens +@SQ SN:GL000201.1 LN:36148 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:dfb7e7ec60ffdcb85cb359ea28454ee9 SP:Homo Sapiens +@SQ SN:GL000247.1 LN:36422 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:7de00226bb7df1c57276ca6baabafd15 SP:Homo Sapiens +@SQ SN:GL000245.1 LN:36651 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:89bc61960f37d94abf0df2d481ada0ec SP:Homo Sapiens +@SQ SN:GL000197.1 LN:37175 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6f5efdd36643a9b8c8ccad6f2f1edc7b SP:Homo Sapiens +@SQ SN:GL000203.1 LN:37498 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:96358c325fe0e70bee73436e8bb14dbd SP:Homo Sapiens +@SQ SN:GL000246.1 LN:38154 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:e4afcd31912af9d9c2546acf1cb23af2 SP:Homo Sapiens +@SQ SN:GL000249.1 LN:38502 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1d78abec37c15fe29a275eb08d5af236 SP:Homo Sapiens +@SQ SN:GL000196.1 LN:38914 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:d92206d1bb4c3b4019c43c0875c06dc0 SP:Homo Sapiens +@SQ SN:GL000248.1 LN:39786 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:5a8e43bec9be36c7b49c84d585107776 SP:Homo Sapiens +@SQ SN:GL000244.1 LN:39929 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:0996b4475f353ca98bacb756ac479140 SP:Homo Sapiens +@SQ SN:GL000238.1 LN:39939 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:131b1efc3270cc838686b54e7c34b17b SP:Homo Sapiens +@SQ SN:GL000202.1 LN:40103 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:06cbf126247d89664a4faebad130fe9c SP:Homo Sapiens +@SQ SN:GL000234.1 LN:40531 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:93f998536b61a56fd0ff47322a911d4b SP:Homo Sapiens +@SQ SN:GL000232.1 LN:40652 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:3e06b6741061ad93a8587531307057d8 SP:Homo Sapiens +@SQ SN:GL000206.1 LN:41001 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:43f69e423533e948bfae5ce1d45bd3f1 SP:Homo Sapiens +@SQ SN:GL000240.1 LN:41933 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:445a86173da9f237d7bcf41c6cb8cc62 SP:Homo Sapiens +@SQ SN:GL000236.1 LN:41934 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:fdcd739913efa1fdc64b6c0cd7016779 SP:Homo Sapiens +@SQ SN:GL000241.1 LN:42152 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:ef4258cdc5a45c206cea8fc3e1d858cf SP:Homo Sapiens +@SQ SN:GL000243.1 LN:43341 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:cc34279a7e353136741c9fce79bc4396 SP:Homo Sapiens +@SQ SN:GL000242.1 LN:43523 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:2f8694fc47576bc81b5fe9e7de0ba49e SP:Homo Sapiens +@SQ SN:GL000230.1 LN:43691 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:b4eb71ee878d3706246b7c1dbef69299 SP:Homo Sapiens +@SQ SN:GL000237.1 LN:45867 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:e0c82e7751df73f4f6d0ed30cdc853c0 SP:Homo Sapiens +@SQ SN:GL000233.1 LN:45941 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:7fed60298a8d62ff808b74b6ce820001 SP:Homo Sapiens +@SQ SN:GL000204.1 LN:81310 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:efc49c871536fa8d79cb0a06fa739722 SP:Homo Sapiens +@SQ SN:GL000198.1 LN:90085 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:868e7784040da90d900d2d1b667a1383 SP:Homo Sapiens +@SQ SN:GL000208.1 LN:92689 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:aa81be49bf3fe63a79bdc6a6f279abf6 SP:Homo Sapiens +@SQ SN:GL000191.1 LN:106433 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:d75b436f50a8214ee9c2a51d30b2c2cc SP:Homo Sapiens +@SQ SN:GL000227.1 LN:128374 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:a4aead23f8053f2655e468bcc6ecdceb SP:Homo Sapiens +@SQ SN:GL000228.1 LN:129120 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:c5a17c97e2c1a0b6a9cc5a6b064b714f SP:Homo Sapiens +@SQ SN:GL000214.1 LN:137718 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:46c2032c37f2ed899eb41c0473319a69 SP:Homo Sapiens +@SQ SN:GL000221.1 LN:155397 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:3238fb74ea87ae857f9c7508d315babb SP:Homo Sapiens +@SQ SN:GL000209.1 LN:159169 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:f40598e2a5a6b26e84a3775e0d1e2c81 SP:Homo Sapiens +@SQ SN:GL000218.1 LN:161147 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1d708b54644c26c7e01c2dad5426d38c SP:Homo Sapiens +@SQ SN:GL000220.1 LN:161802 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:fc35de963c57bf7648429e6454f1c9db SP:Homo Sapiens +@SQ SN:GL000213.1 LN:164239 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:9d424fdcc98866650b58f004080a992a SP:Homo Sapiens +@SQ SN:GL000211.1 LN:166566 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:7daaa45c66b288847b9b32b964e623d3 SP:Homo Sapiens +@SQ SN:GL000199.1 LN:169874 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:569af3b73522fab4b40995ae4944e78e SP:Homo Sapiens +@SQ SN:GL000217.1 LN:172149 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6d243e18dea1945fb7f2517615b8f52e SP:Homo Sapiens +@SQ SN:GL000216.1 LN:172294 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:642a232d91c486ac339263820aef7fe0 SP:Homo Sapiens +@SQ SN:GL000215.1 LN:172545 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:5eb3b418480ae67a997957c909375a73 SP:Homo Sapiens +@SQ SN:GL000205.1 LN:174588 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:d22441398d99caf673e9afb9a1908ec5 SP:Homo Sapiens +@SQ SN:GL000219.1 LN:179198 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:f977edd13bac459cb2ed4a5457dba1b3 SP:Homo Sapiens +@SQ SN:GL000224.1 LN:179693 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:d5b2fc04f6b41b212a4198a07f450e20 SP:Homo Sapiens +@SQ SN:GL000223.1 LN:180455 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:399dfa03bf32022ab52a846f7ca35b30 SP:Homo Sapiens +@SQ SN:GL000195.1 LN:182896 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:5d9ec007868d517e73543b005ba48535 SP:Homo Sapiens +@SQ SN:GL000212.1 LN:186858 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:563531689f3dbd691331fd6c5730a88b SP:Homo Sapiens +@SQ SN:GL000222.1 LN:186861 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6fe9abac455169f50470f5a6b01d0f59 SP:Homo Sapiens +@SQ SN:GL000200.1 LN:187035 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:75e4c8d17cd4addf3917d1703cacaf25 SP:Homo Sapiens +@SQ SN:GL000193.1 LN:189789 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:dbb6e8ece0b5de29da56601613007c2a SP:Homo Sapiens +@SQ SN:GL000194.1 LN:191469 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6ac8f815bf8e845bb3031b73f812c012 SP:Homo Sapiens +@SQ SN:GL000225.1 LN:211173 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:63945c3e6962f28ffd469719a747e73c SP:Homo Sapiens +@SQ SN:GL000192.1 LN:547496 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:325ba9e808f669dfeee210fdd7b470ac SP:Homo Sapiens +@SQ SN:NC_007605 LN:171823 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:NC_007605.1 M5:6743bd63b3ff2b5b8985d8933c53290a SP:Epstein-Barr virus +@PG ID:1 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[N.regions.interval_list, expensive.parsed.interval_list] OUTPUT=joined.regions.interval_list ACTION=UNION PADDING=0 UNIQUE=false SORT=true HEAD=1 SCATTER_COUNT=1 INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@PG ID:2 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[joined.regions.interval_list, exome.evaluation.padded.interval_list] OUTPUT=whole.genome.calling.region.interval_list ACTION=SUBTRACT HEAD=1 INVERT=true PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@CO demo intervals scattered 50-ways +17 25341842 34675848 + interval-526 +17 34725849 62410760 + interval-527 +17 62460761 77546461 + interval-528 +17 77596462 79709049 + interval-529 +17 79759050 81195210 + interval-530 diff --git a/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/44_of_50/scattered.interval_list b/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/44_of_50/scattered.interval_list new file mode 100644 index 0000000..bac3067 --- /dev/null +++ b/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/44_of_50/scattered.interval_list @@ -0,0 +1,92 @@ +@HD VN:1.4 SO:coordinate +@SQ SN:1 LN:249250621 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:1b22b98cdeb4a9304cb5d48026a85128 SP:Homo Sapiens +@SQ SN:2 LN:243199373 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:a0d9851da00400dec1098a9255ac712e SP:Homo Sapiens +@SQ SN:3 LN:198022430 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:fdfd811849cc2fadebc929bb925902e5 SP:Homo Sapiens +@SQ SN:4 LN:191154276 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:23dccd106897542ad87d2765d28a19a1 SP:Homo 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PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[joined.regions.interval_list, exome.evaluation.padded.interval_list] OUTPUT=whole.genome.calling.region.interval_list ACTION=SUBTRACT HEAD=1 INVERT=true PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@CO demo intervals scattered 50-ways +18 10001 15410898 + interval-531 +18 18510899 52059136 + interval-532 +18 52209137 72283353 + interval-533 diff --git a/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/45_of_50/scattered.interval_list b/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/45_of_50/scattered.interval_list new file mode 100644 index 0000000..bf6c515 --- /dev/null +++ b/scripts/utilities/intervals/create_scatter_intervals_demo/output_intervals/45_of_50/scattered.interval_list @@ -0,0 +1,96 @@ +@HD VN:1.4 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UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:dbb6e8ece0b5de29da56601613007c2a SP:Homo Sapiens +@SQ SN:GL000194.1 LN:191469 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6ac8f815bf8e845bb3031b73f812c012 SP:Homo Sapiens +@SQ SN:GL000225.1 LN:211173 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:63945c3e6962f28ffd469719a747e73c SP:Homo Sapiens +@SQ SN:GL000192.1 LN:547496 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:325ba9e808f669dfeee210fdd7b470ac SP:Homo Sapiens +@SQ SN:NC_007605 LN:171823 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:NC_007605.1 M5:6743bd63b3ff2b5b8985d8933c53290a SP:Epstein-Barr virus +@PG ID:1 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[N.regions.interval_list, expensive.parsed.interval_list] 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UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:dbb6e8ece0b5de29da56601613007c2a SP:Homo Sapiens +@SQ SN:GL000194.1 LN:191469 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:6ac8f815bf8e845bb3031b73f812c012 SP:Homo Sapiens +@SQ SN:GL000225.1 LN:211173 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:63945c3e6962f28ffd469719a747e73c SP:Homo Sapiens +@SQ SN:GL000192.1 LN:547496 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:GRCh37 M5:325ba9e808f669dfeee210fdd7b470ac SP:Homo Sapiens +@SQ SN:NC_007605 LN:171823 UR:http://www.broadinstitute.org/ftp/pub/seq/references/Homo_sapiens_assembly19.fasta AS:NC_007605.1 M5:6743bd63b3ff2b5b8985d8933c53290a SP:Epstein-Barr virus +@PG ID:1 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[N.regions.interval_list, expensive.parsed.interval_list] 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M5:6743bd63b3ff2b5b8985d8933c53290a SP:Epstein-Barr virus +@PG ID:1 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[N.regions.interval_list, expensive.parsed.interval_list] OUTPUT=joined.regions.interval_list ACTION=UNION PADDING=0 UNIQUE=false SORT=true HEAD=1 SCATTER_COUNT=1 INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@PG ID:2 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[joined.regions.interval_list, exome.evaluation.padded.interval_list] OUTPUT=whole.genome.calling.region.interval_list ACTION=SUBTRACT HEAD=1 INVERT=true PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@CO demo intervals scattered 50-ways +2 149790583 234003741 + interval-89 diff --git 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SCATTER_COUNT=1 INVERT=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@PG ID:2 PN:IntervalListTools CL:net.sf.picard.util.IntervalListTools INPUT=[joined.regions.interval_list, exome.evaluation.padded.interval_list] OUTPUT=whole.genome.calling.region.interval_list ACTION=SUBTRACT HEAD=1 INVERT=true PADDING=0 UNIQUE=false SORT=true SCATTER_COUNT=1 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false +@CO demo intervals scattered 50-ways +2 234053742 239801978 + interval-90 +2 239831979 240784132 + interval-91 +2 240809133 243102476 + interval-92 +2 243152477 243199373 + interval-93 +3 60001 1695886 + interval-94 +3 1696887 1723886 + interval-95 +3 1724887 1727886 + interval-96 +3 1728887 9889886 + interval-97 diff --git 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