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
gatkexecutable onPATH.
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
gatkexecutable still has to exist for real execution.