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1,255 Open 3,360 Closed
1,255 Open 3,360 Closed
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Issues list

Trying to use NVScoreVariants fails because of python package scorevariants not found
#9190 opened May 28, 2025 by famosab
GenotypeGVCFs - IllegalStateException: VariantContext must contain at least one genotype with likelihoods -- did this VC exceed the max number of alt alleles?
#9186 opened May 26, 2025 by Honeyglitch
Requester pays access issue in Terra workspace
#9183 opened May 20, 2025 by nityajain2002
1
CombineGVCFs produces incorrectly ordered output.
#9181 opened May 20, 2025 by drtconway
CombineGvcfs &GenomicsDBImport
#9178 opened May 19, 2025 by X7xf
Very low CPU usage when running GATK GenotypeGVCFs
#9174 opened May 13, 2025 by GooLey1025
Genotype Germline Sites is Never Unit-tested
#9172 opened May 11, 2025 by DarioS
TransferReadTags is unable to delete temp files
#9169 opened May 7, 2025 by tobsecret
1
Funcotator - Google bucket inaccessible
#9167 opened May 7, 2025 by emsisson
PreprocessIntervals --padding has no effect
#9165 opened May 5, 2025 by lczech
IllegalStateException: Genotype has no likelihoods
#9164 opened May 2, 2025 by aarthi-mohan
Any function to add originial qualities to a BQSR bam?
#9163 opened May 2, 2025 by rajwanir
1
Germline CNV calling error: Cannot run DetermineGermlineContigPloidy due to intability to install gcnvkernel
#9151 opened Apr 16, 2025 by Urja25
1
MUTECT2: allow_potentially_misencoded_quality_scores argument is missing
#9141 opened Apr 11, 2025 by VasLem
1
Mutect2 output VCF fails validation
#9139 opened Apr 10, 2025 by jomoxi
Mutect2 doesn't call SNP despite high coverage and strong evidence unless forced with --alleles
#9137 opened Apr 4, 2025 by PeterResutik
1
Calling somatic mutations with RNA-seq data
#9121 opened Mar 19, 2025 by hukai916
when I use gatk to identify variants in a bam file converted from gam using vg surject, I get error
#9119 opened Mar 13, 2025 by ChenDepp
7
PostprocessGermlineCNVCalls outputs wrong genotyped-segments results
#9111 opened Mar 4, 2025 by DiabloRex
1
Hardcoded HTSJDK JEXL genotype filter bindings not working as expected for VariantFiltration.
#9108 opened Mar 3, 2025 by gokalpcelik
GATK4.5.0.0 HaplotypeCaller exits with error code 245 while no error message
#9104 opened Feb 28, 2025 by Alipha-Clisa
1
GtfToBed errors out with because "gene" is null
#9103 opened Feb 27, 2025 by mmahmoudian
2
Efficiently perform simple merge/append on many VCFs?
#9097 opened Feb 18, 2025 by bbimber
4
negative CNN_1D scores
#9088 opened Feb 4, 2025 by MarionFresquet
2
Miscalling of SNPs and GQ value of 0
#9086 opened Feb 3, 2025 by Sgornard
9
ProTip! Exclude everything labeled bug with -label:bug.