bio-gatk-variant-calling - Call germline variants with GATK
Calls germline SNPs and indels with HaplotypeCaller and GVCF workflows, while covering caller selection, error modeling, and edge cases.
Tags
Updated: 2026-10-07Capabilities
Typical Inputs
Typical Outputs
What this skill does
- Call germline variants
- Generate per-sample GVCFs
- Joint-genotype GVCFs
- Reassemble local haplotypes
- Model read-haplotype likelihoods
- Handle non-diploid samples
- Apply BQSR or DRAGSTR
- Select suitable callers
Inputs
- Reference genome
- Aligned BAM files
- Target intervals
- Known-site resources
- Cohort GVCF files
- Sample analysis context
Outputs
- Variant VCF files
- Per-sample GVCF files
- Joint-genotyped cohort VCF
- Recalibrated BAM files
- Variant-calling recommendations
Requirements
- GATK 4.5 or later
- bcftools 1.19 or later
- Command-line tool access