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Strange HaplotypeCaller behavoir and wrong AD values

Status: Open.

#9227 In broadinstitute/gatk;

· IgorUlitsky opened on Jul 14, 2025

[BUG] Upgrading Funcotator dataset to v1.8.hg38.20230908s causes loss of 'Entrez_Gene_Id' annotation

Status: Open.

#9213 In broadinstitute/gatk;

· SpikyClip opened on Jun 20, 2025

bug: Mutect2 doesn't respect provided --sequence-dictionary

Status: Open.

#9208 In broadinstitute/gatk;

· yfarjoun opened on Jun 15, 2025

MarkDuplicates not respecting --TMP_DIR

Status: Open.

#9205 In broadinstitute/gatk;

· alexnater opened on Jun 12, 2025

Trying to use NVScoreVariants fails because of python package <code>scorevariants</code> not found

Status: Open.

#9190 In broadinstitute/gatk;

· famosab opened on May 28, 2025

GenotypeGVCFs - IllegalStateException: VariantContext must contain at least one genotype with likelihoods -- did this VC exceed the max number of alt alleles?

Status: Open.

#9186 In broadinstitute/gatk;

· Honeyglitch opened on May 26, 2025

Requester pays access issue in Terra workspace

Status: Open.

#9183 In broadinstitute/gatk;

· nityajain2002 opened on May 20, 2025

CombineGVCFs produces incorrectly ordered output.

Status: Open.

#9181 In broadinstitute/gatk;

· drtconway opened on May 20, 2025

CombineGvcfs &amp;GenomicsDBImport

Status: Open.

#9178 In broadinstitute/gatk;

· X7xf opened on May 19, 2025

Very low CPU usage when running GATK GenotypeGVCFs

Status: Open.

#9174 In broadinstitute/gatk;

· GooLey1025 opened on May 13, 2025

Genotype Germline Sites is Never Unit-tested

Status: Open.

#9172 In broadinstitute/gatk;

· DarioS opened on May 11, 2025

TransferReadTags is unable to delete temp files

Status: Open.

#9169 In broadinstitute/gatk;

· tobsecret opened on May 7, 2025