broadinstitute/picard

Clear current search query, filters, and sorts

Make HTSJDK project a proper dependency cleanup
#8 opened May 19, 2014 by heuermh

15
ValidateSamFile should warn that NM validation cannot be done without REFERENCE_SEQUENCE error handling limitation
#258 opened Aug 12, 2015 by jmthibault79

1
Need to handle reverse-complemented indels in LiftoverVcf can of worms limitation
#272 opened Aug 28, 2015 by eitanbanks

2
add percent GQ0 to CollectVariantCallingMetrics feature
#286 opened Sep 15, 2015 by yfarjoun

8
CollectVariantCallingMetrics fails when the VCF has no contig header lines error handling
#298 opened Sep 29, 2015 by nh13

1
Enable RevertSam ATTRIBUTE_TO_CLEAR when REMOVE_ALIGNMENT_INFORMATION=false feature
#300 opened Oct 2, 2015 by ktibbett

11
modify code in CollectInsertSizeMetrics to also collect the actual insert length feature
#343 opened Nov 18, 2015 by yfarjoun

9
Enable COLLECTION_LEVEL argument in CollectSequencingArtifacts Metrics feature
#364 opened Dec 22, 2015 by yfarjoun

1
CollectWgsMetrics should double-check that sequence dictionaries match cleanup error handling
#366 opened Dec 23, 2015 by eitanbanks

3
Add tests to the CrosscheckReadGroupFingerprints functionality tests
#375 opened Jan 7, 2016 by eitanbanks
Add lots of tests for the CheckFingerprint functionality tests
#376 opened Jan 7, 2016 by eitanbanks
CrossCheckReadGroupFingerprints dies with an NPE if a @RG tag is not complete bug cleanup error handling
#383 opened Jan 11, 2016 by yfarjoun
Add DUAL_INDEXED to the list of default adapter sequences feature
#411 opened Jan 22, 2016 by eitanbanks
MarkDuplicates throws error using cram files bug
#433 opened Feb 11, 2016 by dekling

10
Improve CLI help formatting cleanup functions cleanup docs tests
#439 opened Feb 12, 2016 by vdauwera

2
[Bug] When removing duplicates, MarkDuplicates does not remove unmapped records whose mate is a duplicate bug
#451 opened Feb 18, 2016 by sooheelee

2
ValidateSamFile doesn't catch duplicated reads depending on their order bug can of worms
#454 opened Feb 22, 2016 by meganshand

3
Validation errors missing from metric-definitions page docs
#485 opened Mar 17, 2016 by dekling
UpdateVcfSequenceDictionary should handle stdin and stdout gracefully bug cleanup secon
#507 opened Apr 12, 2016 by nh13

24
Picard MarkDuplicates lacks tests regarding the tagging of duplicates. tests
#513 opened Apr 14, 2016 by yfarjoun
Speed up SortSam limitation
#529 opened May 2, 2016 by lmanchon

7
Upstream deletions and CollectVariantCallingMetrics do not play nice right now. can of worms
#555 opened Jun 3, 2016 by yfarjoun

22
MergeBamAlignment creates invalid BAMs in the presence of secondary alignments bug
#589 opened Jul 7, 2016 by tfenne
Make picard build properly even no .git directory is available. cleanup
#605 opened Jul 20, 2016 by lbergelson

6
Picard cannot write to stdout bug
#630 opened Aug 17, 2016 by nh13

2

Previous 1 2 3 Next

ProTip! Type g i on any issue or pull request to go back to the issue listing page.