Variant Calling Nodes

Variant-calling nodes identify SNPs, indels, and structural variants from aligned reads. They expect a coordinate-sorted, de-duplicated BAM and a reference FASTA.

GATK HaplotypeCaller

Industry-standard germline short-variant caller. Performs local de novo assembly of haplotypes in active regions.

Inputs: bam: BAM, reference: FASTA Outputs: vcf: VCF

HaplotypeCaller requires a valid @RG read group on the input BAM. Set it on your aligner node.

GATK Joint Genotyping

Combines per-sample GVCFs and jointly genotypes a cohort.

Inputs: gvcfs: List<VCF>, reference: FASTA Outputs: vcf: VCF

bcftools call

Lightweight, fast variant caller (mpileup + call). Good for bacterial genomes and quick analyses.

Inputs: bam: BAM, reference: FASTA Outputs: vcf: VCF

Filtering & annotation

A complete calling branch

[Mark Duplicates BAM] → [GATK HaplotypeCaller] → [VariantFiltration] → [SnpEff] → [VCF Output]

See also

• Alignment nodes
• Your First Workflow