Skill: genome-variant-calling

Use When

• User wants to call germline variants (SNPs, indels) from a deduplicated BAM.
• User needs to produce a VCF or GVCF for downstream joint genotyping.
• User wants to compare variant callers (GATK HaplotypeCaller vs DeepVariant).
• User is performing WGS or WES variant discovery.

Inputs

• Required:
  • Deduplicated BAM file with index (.bam + .bai).
  • Reference FASTA with .fai index and .dict sequence dictionary.
• Optional:
  • Caller choice: gatk or deepvariant (default: gatk).
  • Intervals or BED file (for WES target regions).
  • GVCF mode flag (emit reference confidence; default: off).
  • Ploidy (default: 2).
  • Output directory (default: current directory).
  • Threads / memory allocation.

Workflow

1. Validate that the BAM is sorted, indexed, and has read groups.
2. If GATK: run gatk HaplotypeCaller with --emit-ref-confidence GVCF (if GVCF mode) or standard VCF output.
3. If DeepVariant: run via Docker or Singularity with the appropriate model type (WGS or WES).
4. If intervals are provided (WES): restrict variant calling to target regions with padding.
5. Index the output VCF/GVCF with bcftools index or gatk IndexFeatureFile.
6. Report variant counts: total variants, SNPs, indels, het/hom ratio, Ti/Tv ratio.

Output Contract

• VCF or gVCF file (.vcf.gz).
• VCF index (.vcf.gz.tbi).
• Variant summary statistics (total, SNPs, indels, het/hom ratio, Ti/Tv).

Limits

• GATK requires Java 17+.
• DeepVariant requires Docker or Singularity (GPU recommended for performance).
• Joint genotyping (GenomicsDBImport + GenotypeGVCFs) is a separate downstream step.
• Memory: ~4 GB per thread for GATK HaplotypeCaller; GPU recommended for DeepVariant.
• This skill handles single-sample calling; multi-sample joint calling is out of scope.
• Common failure cases:
  • BAM missing read groups, causing GATK HaplotypeCaller to reject the input.
  • Reference FASTA lacking .dict or .fai index files.
  • DeepVariant Docker/Singularity image not found or GPU driver mismatch.