Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Soft bed regions v2 #121

Merged
merged 3 commits into from
May 17, 2022
Merged

Soft bed regions v2 #121

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
1afc9c1
Soften the boundaries of the bed file regions for matching variants. …
bnoyvert May 9, 2022
1c84ad9
Add functional tests for --extend
bnoyvert May 16, 2022
45b733c
Increase version number
bnoyvert May 16, 2022
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
53 changes: 53 additions & 0 deletions repo_utils/test_files/answer_key/bench13_extend/fn.vcf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,53 @@
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
##contig=<ID=chr3,length=198295559>
##contig=<ID=chr4,length=190214555>
##contig=<ID=chr5,length=181538259>
##contig=<ID=chr6,length=170805979>
##contig=<ID=chr7,length=159345973>
##contig=<ID=chr8,length=145138636>
##contig=<ID=chr9,length=138394717>
##contig=<ID=chr10,length=133797422>
##contig=<ID=chr11,length=135086622>
##contig=<ID=chr12,length=133275309>
##contig=<ID=chr13,length=114364328>
##contig=<ID=chr14,length=107043718>
##contig=<ID=chr15,length=101991189>
##contig=<ID=chr16,length=90338345>
##contig=<ID=chr17,length=83257441>
##contig=<ID=chr18,length=80373285>
##contig=<ID=chr19,length=58617616>
##contig=<ID=chr20,length=64444167>
##contig=<ID=chr21,length=46709983>
##contig=<ID=chr22,length=50818468>
##contig=<ID=chrX,length=156040895>
##contig=<ID=chrY,length=57227415>
##INFO=<ID=QNAME,Number=1,Type=String,Description="Query name">
##INFO=<ID=QSTART,Number=1,Type=Integer,Description="Query start">
##INFO=<ID=QSTRAND,Number=1,Type=String,Description="Query strand">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##bcftools_mergeVersion=1.10.2+htslib-1.10.2
##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="SV type">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="SV length">
##bcftools_viewVersion=1.12+htslib-1.12
##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021
##FORMAT=<ID=PL,Number=.,Type=Integer,Description='test'>
##FORMAT=<ID=DP,Number=.,Type=Integer,Description='test'>
##INFO=<ID=TruScore,Number=1,Type=Integer,Description="Truvari score for similarity of match">
##INFO=<ID=PctSeqSimilarity,Number=1,Type=Float,Description="Pct sequence similarity between this variant and its closest match">
##INFO=<ID=PctSizeSimilarity,Number=1,Type=Float,Description="Pct size similarity between this variant and its closest match">
##INFO=<ID=PctRecOverlap,Number=1,Type=Float,Description="Percent reciprocal overlap percent of the two calls' coordinates">
##INFO=<ID=StartDistance,Number=1,Type=Integer,Description="Distance of the base call's end from comparison call's start">
##INFO=<ID=EndDistance,Number=1,Type=Integer,Description="Distance of the base call's end from comparison call's end">
##INFO=<ID=SizeDiff,Number=1,Type=Float,Description="Difference in size of base and comp calls">
##INFO=<ID=GTMatch,Number=0,Type=Flag,Description="Base/Comparison Genotypes match">
##INFO=<ID=MatchId,Number=1,Type=String,Description="Id to help tie base/comp calls together {chunkid}.{baseid}.{compid}">
##INFO=<ID=Multi,Number=0,Type=Flag,Description="Call is false due to non-multimatching">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385
chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCATCCCCCGTCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 60 . QNAME=HG002-S9-H1-000001F;QSTART=400044;QSTRAND=+;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.995604;PctSizeSimilarity=0.995595;PctRecOverlap=1;SizeDiff=-1;StartDistance=0;EndDistance=0;TruScore=99;MatchId=6.1.0;Multi GT:PL:DP 1/0:4,8,6:32,9
chr20 642207 . T TGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCAGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGG 60 . QNAME=HG002-S9-H2-000001F;QSTART=596630;QSTRAND=+;SVTYPE=INS;SVLEN=501;PctSeqSimilarity=0.722973;PctSizeSimilarity=0.512974;PctRecOverlap=0.512974;SizeDiff=244;StartDistance=-64;EndDistance=-64;TruScore=58;MatchId=8.0.2 GT:PL:DP 0/1:5,9,1:7,43
chr20 642330 . G GGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGC 60 . QNAME=HG002-S9-H2-000001F;QSTART=597257;QSTRAND=+;SVTYPE=INS;SVLEN=66;PctSeqSimilarity=0.883495;PctSizeSimilarity=0.511628;PctRecOverlap=0;SizeDiff=-63;StartDistance=262;EndDistance=262;GTMatch;TruScore=46;MatchId=8.2.1 GT:PL:DP 0/1:6,1,9:20,25
chr20 709830 . G GACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCGCTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGAACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGGACACTGCTCGGTCCTCCACTCCGTGTGCCCTGTGACCCCCTCATCCTGCCTTTGGATCACGAGCTGGGGTCGGGGGAGGGGATGGTGGGGGGA 60 . QNAME=HG002-S9-H1-000001F;QSTART=689726;QSTRAND=+;SVTYPE=INS;SVLEN=465;PctSeqSimilarity=0.151976;PctSizeSimilarity=0.2;PctRecOverlap=0.202151;SizeDiff=372;StartDistance=71;EndDistance=-22;TruScore=18;MatchId=9.0.0 GT:PL:DP 1/0:4,8,7:50,48
52 changes: 52 additions & 0 deletions repo_utils/test_files/answer_key/bench13_extend/fp.vcf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,52 @@
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
##contig=<ID=chr3,length=198295559>
##contig=<ID=chr4,length=190214555>
##contig=<ID=chr5,length=181538259>
##contig=<ID=chr6,length=170805979>
##contig=<ID=chr7,length=159345973>
##contig=<ID=chr8,length=145138636>
##contig=<ID=chr9,length=138394717>
##contig=<ID=chr10,length=133797422>
##contig=<ID=chr11,length=135086622>
##contig=<ID=chr12,length=133275309>
##contig=<ID=chr13,length=114364328>
##contig=<ID=chr14,length=107043718>
##contig=<ID=chr15,length=101991189>
##contig=<ID=chr16,length=90338345>
##contig=<ID=chr17,length=83257441>
##contig=<ID=chr18,length=80373285>
##contig=<ID=chr19,length=58617616>
##contig=<ID=chr20,length=64444167>
##contig=<ID=chr21,length=46709983>
##contig=<ID=chr22,length=50818468>
##contig=<ID=chrX,length=156040895>
##contig=<ID=chrY,length=57227415>
##INFO=<ID=QNAME,Number=1,Type=String,Description="Query name">
##INFO=<ID=QSTART,Number=1,Type=Integer,Description="Query start">
##INFO=<ID=QSTRAND,Number=1,Type=String,Description="Query strand">
##INFO=<ID=EDGEFLAG,Number=0,Type=Flag,Description="Edge case flags">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##bcftools_mergeVersion=1.10.2+htslib-1.10.2
##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h1-un.arrow-p1.fasta.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__v12_HG00733_hgsvc_pbsq2-clr_1000-flye.h2-un.arrow-p1.fasta.gz.vcf.gz; Date=Thu Jul 22 20:41:33 2021
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="SV type">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="SV length">
##bcftools_viewVersion=1.12+htslib-1.12
##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/unused_samples/grch38/HG00733/exact.vcf.gz; Date=Mon Aug 16 16:57:27 2021
##INFO=<ID=TruScore,Number=1,Type=Integer,Description="Truvari score for similarity of match">
##INFO=<ID=PctSeqSimilarity,Number=1,Type=Float,Description="Pct sequence similarity between this variant and its closest match">
##INFO=<ID=PctSizeSimilarity,Number=1,Type=Float,Description="Pct size similarity between this variant and its closest match">
##INFO=<ID=PctRecOverlap,Number=1,Type=Float,Description="Percent reciprocal overlap percent of the two calls' coordinates">
##INFO=<ID=StartDistance,Number=1,Type=Integer,Description="Distance of the base call's end from comparison call's start">
##INFO=<ID=EndDistance,Number=1,Type=Integer,Description="Distance of the base call's end from comparison call's end">
##INFO=<ID=SizeDiff,Number=1,Type=Float,Description="Difference in size of base and comp calls">
##INFO=<ID=GTMatch,Number=0,Type=Flag,Description="Base/Comparison Genotypes match">
##INFO=<ID=MatchId,Number=1,Type=String,Description="Id to help tie base/comp calls together {chunkid}.{baseid}.{compid}">
##INFO=<ID=Multi,Number=0,Type=Flag,Description="Call is false due to non-multimatching">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT HG00733
chr20 149073 . G GAATCCTGACCCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCA 60 . QNAME=cluster23_scaffold_2;QSTART=25547471;QSTRAND=-;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=0.996154;PctSizeSimilarity=1;PctRecOverlap=0.130435;SizeDiff=0;StartDistance=-60;EndDistance=-60;TruScore=70;MatchId=1.0.1;Multi GT 0/1
chr20 642271 . G GGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGTGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGATGGGGTTGCCTGGGGGGGGGC 60 . QNAME=cluster23_scaffold_3;QSTART=25068731;QSTRAND=-;SVTYPE=INS;SVLEN=257;PctSeqSimilarity=0.722973;PctSizeSimilarity=0.512974;PctRecOverlap=0.512974;SizeDiff=244;StartDistance=-64;EndDistance=-64;TruScore=58;MatchId=8.0.2 GT 1/0
chr20 642068 . G GTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGGGCCCAGCGGGGGTGGGGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCC 60 . QNAME=cluster23_scaffold_2;QSTART=25053097;QSTRAND=-;SVTYPE=INS;SVLEN=129;PctSeqSimilarity=0.883495;PctSizeSimilarity=0.511628;PctRecOverlap=0;SizeDiff=-63;StartDistance=262;EndDistance=262;GTMatch;TruScore=46;MatchId=8.2.1 GT 0/1
chr20 642330 . G GCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGAGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGTGGGGGGCCCAGCGGGGGTGGAGTTGCCTGTGGGGGGGGGGGC 60 . QNAME=cluster23_scaffold_2;QSTART=25052609;QSTRAND=-;SVTYPE=INS;SVLEN=226;PctSeqSimilarity=0.455782;PctSizeSimilarity=0.292035;PctRecOverlap=0.295154;SizeDiff=-160;StartDistance=0;EndDistance=0;GTMatch;TruScore=34;MatchId=8.2.3;Multi GT 0/1
67 changes: 67 additions & 0 deletions repo_utils/test_files/answer_key/bench13_extend/log.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,67 @@
2022-05-16 12:27:07,999 [INFO] Running /mmfs1/groups/res_data/active/bnoyvert/git/truvari-github/truvari/truvari/__main__.py bench -b repo_utils/test_files/input1.vcf.gz -c repo_utils/test_files/input3.vcf.gz -f repo_utils/test_files/reference.fa -o test_results/bench13_extend/ --includebed repo_utils/test_files/include.bed --extend 500
2022-05-16 12:27:08,000 [INFO] Params:
{
"base": "repo_utils/test_files/input1.vcf.gz",
"comp": "repo_utils/test_files/input3.vcf.gz",
"output": "test_results/bench13_extend/",
"reference": "repo_utils/test_files/reference.fa",
"giabreport": false,
"debug": false,
"prog": false,
"refdist": 500,
"pctsim": 0.7,
"minhaplen": 50,
"pctsize": 0.7,
"pctovl": 0.0,
"typeignore": false,
"use_lev": false,
"chunksize": 1000,
"gtcomp": false,
"bSample": null,
"cSample": null,
"sizemin": 50,
"sizefilt": 30,
"sizemax": 50000,
"passonly": false,
"no_ref": false,
"includebed": "repo_utils/test_files/include.bed",
"extend": 500,
"multimatch": false
}
2022-05-16 12:27:08,002 [INFO] Truvari version: 3.3.0-dev
2022-05-16 12:27:08,007 [INFO] Including 11 bed regions
2022-05-16 12:27:08,008 [INFO] Found 1 chromosomes with overlapping regions
2022-05-16 12:27:08,008 [INFO] Extending the regions by 500 bases on each side
2022-05-16 12:27:08,009 [INFO] After region extension found 1 chromosomes with overlapping regions. Merged the overlaps
2022-05-16 12:27:08,084 [INFO] Zipped 2050 variants. Counter({'base': 1130, 'comp': 920})
2022-05-16 12:27:08,084 [INFO] 11 chunks of 2050 variants. Counter({'__filtered': 2025, 'comp': 15, 'base': 10})
2022-05-16 12:27:08,085 [INFO] Stats: {
"TP-base": 6,
"TP-call": 6,
"FP": 4,
"FN": 4,
"precision": 0.6,
"recall": 0.6,
"f1": 0.6,
"base cnt": 10,
"call cnt": 10,
"TP-call_TP-gt": 3,
"TP-call_FP-gt": 3,
"TP-base_TP-gt": 3,
"TP-base_FP-gt": 3,
"gt_concordance": 0.5,
"gt_matrix": {
"(1, 1)": {
"(1, 0)": 1,
"(1, 1)": 2
},
"(0, 1)": {
"(1, 1)": 1,
"(1, 0)": 1
},
"(1, 0)": {
"(1, 0)": 1
}
}
}
2022-05-16 12:27:08,091 [INFO] Finished bench
29 changes: 29 additions & 0 deletions repo_utils/test_files/answer_key/bench13_extend/summary.txt
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,29 @@
{
"TP-base": 6,
"TP-call": 6,
"FP": 4,
"FN": 4,
"precision": 0.6,
"recall": 0.6,
"f1": 0.6,
"base cnt": 10,
"call cnt": 10,
"TP-call_TP-gt": 3,
"TP-call_FP-gt": 3,
"TP-base_TP-gt": 3,
"TP-base_FP-gt": 3,
"gt_concordance": 0.5,
"gt_matrix": {
"(1, 1)": {
"(1, 0)": 1,
"(1, 1)": 2
},
"(0, 1)": {
"(1, 1)": 1,
"(1, 0)": 1
},
"(1, 0)": {
"(1, 0)": 1
}
}
}
55 changes: 55 additions & 0 deletions repo_utils/test_files/answer_key/bench13_extend/tp-base.vcf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,55 @@
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=chr1,length=248956422>
##contig=<ID=chr2,length=242193529>
##contig=<ID=chr3,length=198295559>
##contig=<ID=chr4,length=190214555>
##contig=<ID=chr5,length=181538259>
##contig=<ID=chr6,length=170805979>
##contig=<ID=chr7,length=159345973>
##contig=<ID=chr8,length=145138636>
##contig=<ID=chr9,length=138394717>
##contig=<ID=chr10,length=133797422>
##contig=<ID=chr11,length=135086622>
##contig=<ID=chr12,length=133275309>
##contig=<ID=chr13,length=114364328>
##contig=<ID=chr14,length=107043718>
##contig=<ID=chr15,length=101991189>
##contig=<ID=chr16,length=90338345>
##contig=<ID=chr17,length=83257441>
##contig=<ID=chr18,length=80373285>
##contig=<ID=chr19,length=58617616>
##contig=<ID=chr20,length=64444167>
##contig=<ID=chr21,length=46709983>
##contig=<ID=chr22,length=50818468>
##contig=<ID=chrX,length=156040895>
##contig=<ID=chrY,length=57227415>
##INFO=<ID=QNAME,Number=1,Type=String,Description="Query name">
##INFO=<ID=QSTART,Number=1,Type=Integer,Description="Query start">
##INFO=<ID=QSTRAND,Number=1,Type=String,Description="Query strand">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##bcftools_mergeVersion=1.10.2+htslib-1.10.2
##bcftools_mergeCommand=merge --force-samples -m none /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H1.fa.gz.vcf.gz /users/u233287/scratch/insertion_ref/long_read_data/remap/GRCh38_1kg_mainchrs.fa__NA24385-denovo-H2.fa.gz.vcf.gz; Date=Thu Jul 22 20:43:41 2021
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="SV type">
##INFO=<ID=SVLEN,Number=1,Type=Integer,Description="SV length">
##bcftools_viewVersion=1.12+htslib-1.12
##bcftools_viewCommand=view -r chr20:0-1000000 -O z /home/english/science/english/msru/data/intra_merge/grch38/li/NA24385/exact.vcf.gz; Date=Mon Aug 16 16:45:51 2021
##FORMAT=<ID=PL,Number=.,Type=Integer,Description='test'>
##FORMAT=<ID=DP,Number=.,Type=Integer,Description='test'>
##INFO=<ID=TruScore,Number=1,Type=Integer,Description="Truvari score for similarity of match">
##INFO=<ID=PctSeqSimilarity,Number=1,Type=Float,Description="Pct sequence similarity between this variant and its closest match">
##INFO=<ID=PctSizeSimilarity,Number=1,Type=Float,Description="Pct size similarity between this variant and its closest match">
##INFO=<ID=PctRecOverlap,Number=1,Type=Float,Description="Percent reciprocal overlap percent of the two calls' coordinates">
##INFO=<ID=StartDistance,Number=1,Type=Integer,Description="Distance of the base call's end from comparison call's start">
##INFO=<ID=EndDistance,Number=1,Type=Integer,Description="Distance of the base call's end from comparison call's end">
##INFO=<ID=SizeDiff,Number=1,Type=Float,Description="Difference in size of base and comp calls">
##INFO=<ID=GTMatch,Number=0,Type=Flag,Description="Base/Comparison Genotypes match">
##INFO=<ID=MatchId,Number=1,Type=String,Description="Id to help tie base/comp calls together {chunkid}.{baseid}.{compid}">
##INFO=<ID=Multi,Number=0,Type=Flag,Description="Call is false due to non-multimatching">
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA24385
chr20 149013 . A ACCATATTTGGGAGGCAATTTTACCTGTTCTCAAGGCCGCATCTCTACCCCATCTCATGCGAATCCTGAC 60 . QNAME=HG002-S9-H1-000001F;QSTART=127907;QSTRAND=+;SVTYPE=INS;SVLEN=69;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=1.0.0 GT:PL:DP 1/1:8,8,5:15,29
chr20 306268 . A ACCAGGCTGGAGTGCAGTGGCTCACTGCGTGGCTCGCTACAGCCTACAACTCCTGGGCTCCAGCAATCCTGCTGCCCCAGCCTCCTGTGTAACTGAGACTACAGGCACGCACCACCACACCCAGCTAATTTTTTCTTTCTTTTTTTTTTTTTTGAGATGAACTCTCACTCTGTTGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=285475;QSTRAND=+;SVTYPE=INS;SVLEN=175;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=4.0.0 GT:PL:DP 1/1:2,7,2:17,31
chr20 420665 . G GCCCACCCCATCCCCCGTCCCCATCCCCCATCCCCCGTCCCCCGTCCCCATCCCCCGTCCCCCATCTCCTGTCCCCCGTCCCCATCCCCCGTCCCCCGTCCCCCATCCCATCCCCCACCCCCATCCCCCGTCCCCCGTCCCCATCCCCCATCCCCCATCCCCCATCCCCCGTCCGCCGTCCCCCATCTCCTGTCCCCCGTCCCCCATCCCCCGTCCCCATCCCCCACC 61 . QNAME=HG002-S9-H2-000001F;QSTART=374905;QSTRAND=+;SVTYPE=INS;SVLEN=227;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=6.0.0 GT:PL 0/1:.
chr20 613783 . TGTGTGCTGAGTCCAGCTCAAGTCCCTTGGTTCCCACTGCTGCTAAGCATGCACG T 60 . QNAME=HG002-S9-H1-000001F;QSTART=593293;QSTRAND=+;SVTYPE=DEL;SVLEN=-54;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;GTMatch;TruScore=100;MatchId=7.0.0 GT:PL:DP 1/1:6,8,8:40,41
chr20 642300 . G GCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGCCCAGCGGGGGTGGAGTTGCCTGGGGGGGGGGC 60 . QNAME=HG002-S9-H1-000001F;QSTART=621812;QSTRAND=+;SVTYPE=INS;SVLEN=408;PctSeqSimilarity=0.890591;PctSizeSimilarity=0.789216;PctRecOverlap=0.672372;SizeDiff=86;StartDistance=-91;EndDistance=-91;GTMatch;TruScore=78;MatchId=8.1.4 GT:PL:DP 1/0:5,10,5:44,36
chr20 949516 . CTCTGAAGAGGTAACATTTGAACTGAGATGTAGAGGGAGAGAAGGAACTAGCCATGTGGAGATCTGGGGGAGGAGCATTCCAGGCAGAGGGGATAGCAAGTGCA C 60 . QNAME=HG002-S9-H2-000001F;QSTART=905663;QSTRAND=+;SVTYPE=DEL;SVLEN=-103;PctSeqSimilarity=1;PctSizeSimilarity=1;PctRecOverlap=1;SizeDiff=0;StartDistance=0;EndDistance=0;TruScore=100;MatchId=10.0.0 GT:PL:DP 0/1:6,6,1:34,8