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MUTECT2: allow_potentially_misencoded_quality_scores argument is missing

Status: Open.

#9141 In broadinstitute/gatk;

· VasLem opened on Apr 11, 2025

Fix critical vulnerability (CVSS score 10) caused by Parquet-Avro library

Status: Open.

#9140 In broadinstitute/gatk;

· JWollnik opened on Apr 11, 2025

Mutect2 output VCF fails validation

Status: Open.

#9139 In broadinstitute/gatk;

· jomoxi opened on Apr 10, 2025

Mutect2 doesn't call SNP despite high coverage and strong evidence unless forced with --alleles

Status: Open.

#9137 In broadinstitute/gatk;

· PeterResutik opened on Apr 4, 2025

Calling somatic mutations with RNA-seq data

Status: Open.

#9121 In broadinstitute/gatk;

· hukai916 opened on Mar 19, 2025

when I use gatk to identify variants in a bam file converted from gam using vg surject, I get error

Status: Open.

#9119 In broadinstitute/gatk;

· ChenDepp opened on Mar 13, 2025

PostprocessGermlineCNVCalls outputs wrong genotyped-segments results

Status: Open.

#9111 In broadinstitute/gatk;

· DiabloRex opened on Mar 4, 2025

Hardcoded HTSJDK JEXL genotype filter bindings not working as expected for VariantFiltration.

Status: Open.

#9108 In broadinstitute/gatk;

· gokalpcelik opened on Mar 3, 2025

GATK4.5.0.0 HaplotypeCaller exits with error code 245 while no error message

Status: Open.

#9104 In broadinstitute/gatk;

· Alipha-Clisa opened on Feb 28, 2025

GtfToBed errors out with because "gene" is null

Status: Open.

#9103 In broadinstitute/gatk;

· mmahmoudian opened on Feb 27, 2025

Efficiently perform simple merge/append on many VCFs?

Status: Open.

#9097 In broadinstitute/gatk;

· bbimber opened on Feb 18, 2025

negative CNN_1D scores

Status: Open.

#9088 In broadinstitute/gatk;

· MarionFresquet opened on Feb 4, 2025