name	gatk-genotypegvcfs
description	Use when joint-genotyping one or more germline gVCFs into a cohort VCF with GATK GenotypeGVCFs.
disable-model-invocation	true
user-invocable	true

gatk-genotypegvcfs

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.

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.

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

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.

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name	gatk-genotypegvcfs
description	Use when joint-genotyping one or more germline gVCFs into a cohort VCF with GATK GenotypeGVCFs.
disable-model-invocation	true
user-invocable	true

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.

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.

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

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.