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Pull requests: broadinstitute/picard

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28 Open 1,145 Closed
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Pull requests list

docs: fix MarkDuplicates option name
#2051 opened Jun 7, 2026 by titanniya542-spec Loading…
1 of 5 tasks
1
1
MarkDuplicates: add opt-in TAG_DUPLICATE_KEY emitting canonical fragment key (kf) feature
#2049 opened Jun 2, 2026 by tfenne Collaborator Loading…
2 of 5 tasks
@tfenne
1
LiftoverVcf: add optional PROGRESS_JSON NDJSON sidecar output
#2048 opened May 16, 2026 by carstenerickson Loading…
1
1
LiftoverVcf: log live reject rate alongside ProgressLogger milestones
#2047 opened May 16, 2026 by carstenerickson Loading…
1
switches from short to int for tile number
#2044 opened May 2, 2026 by bwlang Contributor Loading…
2 of 5 tasks
Fix to CollectSamErrorMetrics getIndelOperator function to check operator type
#2041 opened Mar 24, 2026 by tfenne Collaborator Loading…
2 of 5 tasks
1
Fix UMI-aware duplicate set tagging
#2040 opened Mar 11, 2026 by lawremi Loading…
2 of 5 tasks
LiftoverVcf - Use indexed FASTA access in LiftoverVcf for faster reference loading
#2038 opened Mar 10, 2026 by anticni Loading…
1 of 5 tasks
1
Add molecular position stratification to CollectSamErrorMetrics
#2035 opened Feb 3, 2026 by yfarjoun Contributor Loading…
5 tasks
5
added parallelization to the actual cross-checking part of Crosscheck…
#2033 opened Jan 29, 2026 by yfarjoun Contributor • Draft
2
Add draft CONTRIBUTING.md file.
#2031 opened Jan 20, 2026 by yfarjoun Contributor Loading…
2
Filter reads for gc bias (mapq and interval)
#2030 opened Jan 9, 2026 by bwlang Contributor Loading…
3 of 5 tasks
26
Htsjdk Beta API first usage
#1981 opened Nov 22, 2024 by lbergelson Contributor Loading…
FLOW_* parameters must be accompanied by FLOW_MODE
#1980 opened Oct 13, 2024 by dror27 Contributor Loading…
@lbergelson
2
Refactor code around cloud support
#1975 opened Aug 9, 2024 by takutosato Contributor Loading…
5 tasks
19
Fold80 Bug Fix
#1972 opened Jul 31, 2024 by Patrick-Schlaeger-Broad • Draft
5 tasks
Add new argument to allow setting the google requester pays project
#1938 opened Jan 11, 2024 by lbergelson Contributor Loading…
1
@lbergelson
5
Test updating to java 21
#1931 opened Dec 19, 2023 by lbergelson Contributor • Draft
Cloud support for BuildBamIndex outputs.
#1925 opened Dec 4, 2023 by cmnbroad Contributor • Draft
2
@takutosato
1
DRAFT: VCFHeader refactoring
#1880 opened May 17, 2023 by cmnbroad Contributor • Draft
@droazen @cmnbroad
Enables setting the google-project that will be charged for requests …
#1825 opened Aug 23, 2022 by yfarjoun Contributor Loading…
@lbergelson
11
Account for overlapping reads in Theoretical Sensitivity model
#1802 opened Apr 26, 2022 by fleharty Contributor Loading…
2 of 5 tasks
25
Make truncating the histogram optional in CollectInsertSizeMetrics
#1779 opened Feb 25, 2022 by takutosato Contributor Loading…
1 of 5 tasks
@takutosato
20
Consider "low" mapping quality reads to be unaligned for the purpose of Marking Duplicates.
#1460 opened Feb 2, 2020 by yfarjoun Contributor Loading…
5 tasks
1
@fleharty
8
Partial fix of coordinate casting to short in MarkDuplicates
#1442 opened Dec 13, 2019 by yfarjoun Contributor Loading…
5 tasks
11
ProTip! Exclude everything labeled bug with -label:bug.