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1,186 Open 3,316 Closed
1,186 Open 3,316 Closed
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Issues list

VariantAnnotator IndexOutOfBoundsException
#8800 opened Apr 30, 2024 by ykcchong
1 of 2 tasks
Prevent users enabling annotations with mismatching data type (flow etc)
#8788 opened Apr 22, 2024 by gokalpcelik
1
@droazen @lbergelson
@jamesemery @ilyasoifer @gokalpcelik
6
GenotypeGVCFs report java.lang.OutOfMemoryError: Java heap space while call incremental imported GenomicsDB
#8777 opened Apr 16, 2024 by LYOKOIIIYYR
3
PrintReads introduces N bases when encoding some CRAMs and changes sequence cram PRIORITY_HIGH
#8768 opened Apr 9, 2024 by ilyasoifer
1 task
@cmnbroad @meganshand
11
ApplyVQSR Exception thrown at a/some variation site(s) after INDEL VQSR
#8767 opened Apr 9, 2024 by Dkyuan
Using PathSeqFilterSpark --ignore-alignment-contigs raises error
#8766 opened Apr 7, 2024 by abdohlman
Bug in NIO library using public reference files ending in .fa.gz
#8751 opened Mar 25, 2024 by rickymagner
1 task done
GATK VariantsToTable: QUAL="." in input becomes QUAL="-10.0" in output
#8748 opened Mar 22, 2024 by friedav
How to avoid java.lang.ArrayIndexOutOfBoundsException when indexing a vcf.gz file?
#8747 opened Mar 21, 2024 by erah1
2 tasks
GCNV: AssertionError: Loaded mean for "log_mean_bias_t" has an unexpected shape; loaded: (11903,), expected: (11901,)
#8740 opened Mar 14, 2024 by stefandiederich
java.io.IOException: Transport endpoint is not connected
#8735 opened Mar 13, 2024 by TYU1201
Add toggle for treatment of MNPs in VETS.
#8733 opened Mar 12, 2024 by samuelklee
@samuelklee
Memory issues when running BaseRecalibrator
#8726 opened Mar 9, 2024 by MetteBoge
Multiple Tools (Documentation): Format of --arguments_file
#8722 opened Mar 7, 2024 by J-Moravec
SelectVariants (Documentation): Purpose of reference sequence
#8721 opened Mar 7, 2024 by J-Moravec
Bug Funcotator: wrong canonical
#8714 opened Mar 5, 2024 by zhanyinx
1
GenotypeGVCFs - A USER ERROR has occurred: Couldn't create GenomicsDBFeatureReader
#8709 opened Mar 1, 2024 by StefanoPallotti
1
Mutect2 is incompatible with Mutect2 VCFs as feature files
#8699 opened Feb 20, 2024 by lculibrk
Docker image (broadinstitute/gatk) has too many unnecessary layers potentially causing throttling issues
#8684 opened Feb 8, 2024 by MattMcL4475
8
GenomicsDB malloc unaligned tcache chunk error GenomicsDB
#8683 opened Feb 7, 2024 by danagibbon
@nalinigans
8
Fix broken links in HaplotypeCaller documentation
#8682 opened Feb 7, 2024 by droazen
@kockan
does GATK offers to match alleles in two vcf files?
#8681 opened Feb 7, 2024 by RezwanCAAS
FileDataSource is in SAMRecord
#8671 opened Jan 31, 2024 by LeeTL1220
1 task done
1
VariantRecalibrator R-script fails if scales v1.3.0 is installed bug
#8664 opened Jan 23, 2024 by MikkelSchubert
1 of 2 tasks
6
GetPileupSummaries Permanently Stalled but High CPU Usage
#8654 opened Jan 12, 2024 by DarioS
5
ProTip! What’s not been updated in a month: updated:<2024-04-08.