broadinstitute/picard

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Discussion around command line parser changes
#786 opened Apr 5, 2017 by cmnbroad

31
UpdateVcfSequenceDictionary should handle stdin and stdout gracefully bug cleanup secon
#507 opened Apr 12, 2016 by nh13

24
Upstream deletions and CollectVariantCallingMetrics do not play nice right now. can of worms
#555 opened Jun 3, 2016 by yfarjoun

22
RevertSam, when REMOVE_ALIGNMENT_INFORMATION=true, should not stall on sam validation errors
#849 opened Jun 30, 2017 by sooheelee 1 of 1

21
Make HTSJDK project a proper dependency cleanup
#8 opened May 19, 2014 by heuermh

15
Soliciting feedback on plans to merge Picard + GATK4
#647 opened Sep 8, 2016 by vdauwera

12
Enable RevertSam ATTRIBUTE_TO_CLEAR when REMOVE_ALIGNMENT_INFORMATION=false feature
#300 opened Oct 2, 2015 by ktibbett

11
MarkDuplicates throws error using cram files bug
#433 opened Feb 11, 2016 by dekling

10
modify code in CollectInsertSizeMetrics to also collect the actual insert length feature
#343 opened Nov 18, 2015 by yfarjoun

9
picard SortVcf and MergeVcfs: do not reorder INFO column contens and header rows
#760 opened Feb 21, 2017 by mmokrejs

9
UpdateVcfSequenceDictionary cannot write index bug
#863 opened Jul 10, 2017 by nh13

9
add percent GQ0 to CollectVariantCallingMetrics feature
#286 opened Sep 15, 2015 by yfarjoun

8
GTF to Refflat tool for use with CollectRnaSeqMetrics feature
#805 opened Apr 27, 2017 by nh13

7
CollectIlluminaLaneMetrics does not handle read structures with molecular indexes bug
#688 opened Nov 17, 2016 by nh13

7
Speed up SortSam limitation
#529 opened May 2, 2016 by lmanchon

7
Make picard build properly even no .git directory is available. cleanup
#605 opened Jul 20, 2016 by lbergelson

6
Add CheckFingerprint to the list of documentation targets in build.gradle docs
#774 opened Mar 13, 2017 by sooheelee

6
Cannot index bam from reference with any contig > 512M limitation
#706 opened Dec 9, 2016 by vdauwera

5
Index creation should work when running GatherVcfs on block compressed VCFs
#789 opened Apr 7, 2017 by vdauwera

4
custom adapters with IlluminaBasecallsToSam
#790 opened Apr 10, 2017 by jdc8890

4
How should I cite picard when refering to its use on a paper?
#808 opened May 4, 2017 by el42008 0 of 2

4
CollectRnaSeqMetrics report very low rRNA RIBOSOMAL_BASES
#841 opened Jun 17, 2017 by wangyugui

4
Should CollectHsMetrics also emit PCT@5x? secon Vanilla
#852 opened Jul 5, 2017 by yfarjoun

4
User-defined coverage in CollectHsMetrics
#851 opened Jul 3, 2017 by Anupriya014

4
Clarify in documentation that ScatterIntervalsByNs requires index and dictionary
#802 opened Apr 26, 2017 by sooheelee

3

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