Skip to content

Issues: broadinstitute/picard

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

200 Open 606 Closed
200 Open 606 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

FOLD_80_BASE_PENALTY Metric from TargetMetricsCollector does not exclude 0 coverage regions.
#1971 opened Jul 30, 2024 by Patrick-Schlaeger-Broad
Can CollectWgsMetrics fall back to slow algorithm gracefully if the fast one fails with the default read length?
#1970 opened Jul 8, 2024 by gokalpcelik
8
ValidateSamFile wrong NM tag computation
#1963 opened May 29, 2024 by albertocasagrande
1 of 2 tasks
@kockan
3
--USE_END_IN_UNPAIRED_READS and --USE_UNPAIRED_CLIPPED_END options for picard MarkDuplicates have no effect
#1959 opened Apr 16, 2024 by ChrisHIV
12
MarkDuplicates with single end data does not write the full report
#1944 opened Feb 20, 2024 by mattsoup
1 of 2 tasks
@kockan
3
Streaming from requester-pays buckets for CrosscheckFingerprints doesn't work in Terra
#1927 opened Dec 14, 2023 by rickymagner
1
@lbergelson
2
Conda installer
#1897 opened Jul 4, 2023 by lappazos
@droazen
8
Order of rows in crosscheck metrics files are non-deterministic
#1854 opened Feb 1, 2023 by kachulis
1
4
BuildBamIndex creates index file in the current directory
#1827 opened Sep 9, 2022 by ghost
1
9
Documentation request: Better examples of the inputs to ExtractIlluminaBarcodes, IlliminaBasecallsToFastq, and IlluminaBasecallsToSam
#1815 opened Jun 30, 2022 by bkohrn
CollectMultipleMetrics Skip making charts if R is not installed R-Dependency
#1808 opened May 19, 2022 by nh13
1
Filter HOM_REF records without GQ information
#1805 opened May 14, 2022 by biozzq
Bug report: A fatal error has been detected by the Java Runtime Environment
#1803 opened Apr 27, 2022 by Programjackanapes
3
ExtractIlluminaBarcodes opening a lot of files, error "Too many open files"
#1801 opened Apr 25, 2022 by GATKSupportTeam
2
Picard not finishing jobs on ArchLinux when using parallel - BUG
#1798 opened Apr 17, 2022 by GACGAMA
IntervalListToolsTest.testScatterByContent and IntervalListToolsTest.testScatter could use some improvement
#1795 opened Apr 7, 2022 by kachulis
Don't fail if R is not installed R-Dependency
#1793 opened Apr 6, 2022 by paidi
1
LiftOver stuck after starting
#1790 opened Apr 3, 2022 by JavierMenRev
MergeBamAlignment conflicting headers between mapped and unmapped
#1789 opened Mar 30, 2022 by GATKSupportTeam
Immediately stop with input string error (NumberFormatException: For input string)
#1783 opened Mar 10, 2022 by JuiTse
8
IlluminaBasecallsToSam raises unexpected exception with an index out of bounds access (race condition?)
#1781 opened Mar 3, 2022 by clintval
MergeBamAlignment outputting all mapped and unmapped records
#1778 opened Feb 18, 2022 by stkgo
1 task done
1
Picard SortVcf has issues reading from /dev/stdin and writing to /dev/stdout stdin/stdout
#1776 opened Feb 14, 2022 by clintval
IlluminaBasecallsToSam skipping barcodes
#1774 opened Jan 27, 2022 by nchernia
5
Deterioration of IlluminaBasecallsToSam performance and memory usage over the past year
#1771 opened Jan 18, 2022 by alecw
1 task
6
ProTip! What’s not been updated in a month: updated:<2024-10-10.