Gatk Genotypegvcfs

Use when joint-genotyping one or more germline gVCFs into a cohort VCF with GATK GenotypeGVCFs.

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gatk-genotypegvcfs

Quick Start

  • Command: gatk GenotypeGVCFs
  • Local executable: /home/vimalinx/miniforge3/envs/bio/bin/gatk
  • Install hint: Install GATK into the active bioinformatics environment or put a working gatk executable on PATH.

When To Use This Tool

  • Joint-genotyping per-sample gVCFs into a cohort VCF.
  • Standard downstream step after producing reference-confidence gVCFs with HaplotypeCaller.
  • Germline SNP/indel discovery workflows for WES or WGS cohorts.

Common Patterns

gatk GenotypeGVCFs \
  -R reference.fa \
  -V cohort.g.vcf.gz \
  -O cohort.joint.vcf.gz

Guardrails

  • Input gVCFs must have been generated against the same reference build and compatible interval scheme.
  • This skill definition only proves the workflow step is known; the local gatk executable still has to exist for real execution.

vimalinx/bio-agent/tree/main/.claude/skills/gatk-genotypegvcfs commit 471c298131

Frequently asked questions

npx skillmds add vimalinx/gatk-genotypegvcfs