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Issues list

HsMetrics PCT_USABLE_BASES_ON_BAIT definition/calculation error
#1996 opened Feb 7, 2025 by ioguztuncay
CollectSamErrorMetrics (ERROR accumulator) doesn't understand lowercased reference bases
#1994 opened Feb 7, 2025 by yfarjoun
1
CollectMultipleMetrics does not accept RIBOSOMAL_INTERVALS
#1991 opened Feb 5, 2025 by Redmar-van-den-Berg
1
Merging of previously sorted BAM files
#1990 opened Jan 29, 2025 by fgvieira
Test accuracy should be relaxed for picard.analysis.directed.CollectHsMetricsTest.testHsMetricsF80DoesNotUseCovCap
#1987 opened Dec 26, 2024 by pgrt
FOLD_80_BASE_PENALTY Metric from TargetMetricsCollector does not exclude 0 coverage regions.
#1971 opened Jul 30, 2024 by Patrick-Schlaeger-Broad
@kachulis
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
@rickymagner
9
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
ProTip! What’s not been updated in a month: updated:<2025-01-09.