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Pull requests: broadinstitute/picard
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docs: fix MarkDuplicates option name
#2051
opened Jun 7, 2026 by
titanniya542-spec
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1 of 5 tasks
MarkDuplicates: add opt-in TAG_DUPLICATE_KEY emitting canonical fragment key (kf)
feature
#2049
opened Jun 2, 2026 by
tfenne
Collaborator
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2 of 5 tasks
LiftoverVcf: add optional PROGRESS_JSON NDJSON sidecar output
#2048
opened May 16, 2026 by
carstenerickson
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LiftoverVcf: log live reject rate alongside ProgressLogger milestones
#2047
opened May 16, 2026 by
carstenerickson
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switches from short to int for tile number
#2044
opened May 2, 2026 by
bwlang
Contributor
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2 of 5 tasks
Fix to CollectSamErrorMetrics getIndelOperator function to check operator type
#2041
opened Mar 24, 2026 by
tfenne
Collaborator
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2 of 5 tasks
LiftoverVcf - Use indexed FASTA access in LiftoverVcf for faster reference loading
#2038
opened Mar 10, 2026 by
anticni
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1 of 5 tasks
Add molecular position stratification to CollectSamErrorMetrics
#2035
opened Feb 3, 2026 by
yfarjoun
Contributor
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5 tasks
Filter reads for gc bias (mapq and interval)
#2030
opened Jan 9, 2026 by
bwlang
Contributor
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3 of 5 tasks
FLOW_* parameters must be accompanied by FLOW_MODE
#1980
opened Oct 13, 2024 by
dror27
Contributor
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Refactor code around cloud support
#1975
opened Aug 9, 2024 by
takutosato
Contributor
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5 tasks
Add new argument to allow setting the google requester pays project
#1938
opened Jan 11, 2024 by
lbergelson
Contributor
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Enables setting the google-project that will be charged for requests …
#1825
opened Aug 23, 2022 by
yfarjoun
Contributor
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Account for overlapping reads in Theoretical Sensitivity model
#1802
opened Apr 26, 2022 by
fleharty
Contributor
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2 of 5 tasks
Make truncating the histogram optional in CollectInsertSizeMetrics
#1779
opened Feb 25, 2022 by
takutosato
Contributor
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1 of 5 tasks
Consider "low" mapping quality reads to be unaligned for the purpose of Marking Duplicates.
#1460
opened Feb 2, 2020 by
yfarjoun
Contributor
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5 tasks
Partial fix of coordinate casting to short in MarkDuplicates
#1442
opened Dec 13, 2019 by
yfarjoun
Contributor
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5 tasks
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