broadinstitute/picard

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Add option to output gzipped FASTQ in SamToFastq
#873 opened Jul 17, 2017 by pplettner

3
picard-2.10.2: Failed to apply plugin [id 'org.ajoberstar.grgit']
#872 opened Jul 15, 2017 by mmokrejs
incorrect tests were removed from the deprecated CrossChekReadgroupFingerprint
#869 opened Jul 13, 2017 by yfarjoun
More communication about planned and released changes to Picard functionality docs
#866 opened Jul 12, 2017 by alecw
UpdateVcfSequenceDictionary cannot write index bug
#863 opened Jul 10, 2017 by nh13

9
Resurrect Picard docker repo and populate with images of new versions
#857 opened Jul 6, 2017 by vdauwera

3
use Static file endings for ".vcf", ".bcf", ".vcf.gz"
#854 opened Jul 5, 2017 by yfarjoun
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
RevertSam, when REMOVE_ALIGNMENT_INFORMATION=true, should not stall on sam validation errors
#849 opened Jun 30, 2017 by sooheelee 1 of 1

21
SetNmMdAndUqTags needs to compare the SAM file's dictionary to the reference's
#845 opened Jun 21, 2017 by ronlevine

1
CollectRnaSeqMetrics report very low rRNA RIBOSOMAL_BASES
#841 opened Jun 17, 2017 by wangyugui

4
A formal request to share the human HAPLOTYPE_MAP resource
#837 opened Jun 15, 2017 by sooheelee
Rev Htsjdk and fix the build error.
#815 opened May 16, 2017 by yfarjoun 0 of 2
How to tell if VCFFileReader has an index?
#814 opened May 16, 2017 by yfarjoun

1
Include OpenJDK in tests to be compatible with Docker
#813 opened May 11, 2017 by sooheelee 0 of 2

1
How should I cite picard when refering to its use on a paper?
#808 opened May 4, 2017 by el42008 0 of 2

4
GTF to Refflat tool for use with CollectRnaSeqMetrics feature
#805 opened Apr 27, 2017 by nh13

7
Clarify in documentation that ScatterIntervalsByNs requires index and dictionary
#802 opened Apr 26, 2017 by sooheelee

3
MergeSamFiles accept SO:UNKNOWN
#796 opened Apr 20, 2017 by MichelMoser
custom adapters with IlluminaBasecallsToSam
#790 opened Apr 10, 2017 by jdc8890

4
Index creation should work when running GatherVcfs on block compressed VCFs
#789 opened Apr 7, 2017 by vdauwera

4
Combine CollectWgsMetrics and CollectRawWgsMetricsby a locus-iterating collector
#788 opened Apr 7, 2017 by vdauwera

2
wrong filtering in Alignment metrics
#787 opened Apr 6, 2017 by renkyp

1
Discussion around command line parser changes
#786 opened Apr 5, 2017 by cmnbroad

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