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ChoCallate

ChoCallate (Chorus of Callers) is a Nextflow pipeline for consensus-based variant calling. It maps FASTQ reads or accepts aligned BAMs, calls variants with bcftools, FreeBayes and GATK, and applies a configurable consensus rule to produce high-confidence SNVs and indels.

This documentation targets ChoCallate 4.0.1.

Documentation

• Installing ChoCallate
• Pipeline overview
• Inputs and reference
• CLI reference
• Consensus model
• Output structure
• Merge strategies and testing
• Operations and troubleshooting
• Testing and CI
• Developer guide

Source code, releases and changelog: alermol/ChoCallate | CHANGELOG.

Pipeline at a glance

1. Read mapping with Bowtie2, BWA or Minimap2 (skipped for BAM input).
2. Shared BAM post-processing: mate fixing, sorting, duplicate handling, MAPQ filtering, optional left-alignment and one CSI index.
3. Coverage BED generation with mosdepth, restricted by include_bed and exclude_bed.
4. Variant calling with the configured callers on shared intervals.
5. Consensus generation over every covered position, with two-stage voting.
6. Optional multi-sample merge and final BCF/VCF export.

Inputs and outputs

Inputs: FASTQ (paired-end, single-end or mixed) or a pre-aligned BAM; a plain or bgzip-compressed reference FASTA; mapper indexes for FASTQ input; optional include/exclude BED files.

Outputs: one merged or per-sample consensus BCF/VCF, mapping statistics, dropped_samples.txt, and standard Nextflow reports. All covered sites are written by default, including monomorphic positions.

Start with Installing ChoCallate, then configure a run with the CLI reference. See Output structure for the exact files, header metadata and FORMAT/INFO fields.