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ChoCallate (Chorus of Callers) is a Nextflow pipeline for consensus-based variant calling. It combines results from multiple variant callers and applies configurable consensus rules to produce high-confidence SNVs and indels.

What you provide

• Reads: FASTQs, or a pre-aligned BAM (if you provide a BAM, read mapping is skipped)
• Reference genome: FASTA (plus any indexes required by the selected tools)

What you get

• Consensus variant calls: BCF and/or VCF (depending on options)
• Reports and logs: per-step outputs for troubleshooting

Workflow overview

• (Optional) Read mapping
• BAM preprocessing: filtering, (optional) duplicate marking, (optional) indel left-alignment
• Variant calling with multiple callers
• Consensus generation
• (Optional) Merge caller outputs
• (Optional) Convert BCF → VCF