wf-human-snp documentation
1 min

Diploid small variant calling workflow

This repository contains a nextflow workflow for performing diploid variant calling of whole genome data.


This workflow uses Clair3 for calling small variants from long reads. Clair3 makes the best of two methods: pileup (for fast calling of variant candidates in high confidence regions), and full-alignment (to improve precision of calls of more complex candidates).

The workflow will output a gzipped VCF file containing small variants found in the dataset.


The workflow uses nextflow to manage compute and software resources, as such nextflow will need to be installed before attempting to run the workflow.

The workflow can currently be run using either Docker or conda to provide isolation of the required software. Both methods are automated out-of-the-box provided either docker of conda is installed.

It is not required to clone or download the git repository in order to run the workflow. For more information on running EPI2ME Labs workflows visit out website.

Workflow options

To obtain the workflow, having installed nextflow, users can run:

nextflow run epi2me-labs/wf-human-snp --help

to see the workflow options and their descriptions.

Download demonstration data

A small test dataset is provided for the purposes of testing the workflow software, it can be downloaded using:

wget -O demo_data.tar.gz \
tar -xzvf demo_data.tar.gz

The workflow can be run with the demonstration data using:

nextflow run epi2me-labs/wf-human-snp \
    -w ${OUTPUT}/workspace \
    -profile standard \
    --bam demo_data/chr6_chr20.bam \
    --bed demo_data/chr6_chr20.bed \
    --ref demo_data/chr6_chr20.fasta \
    --out_dir ${OUTPUT}

The output of the pipeline will be found in ./output for the above example. This directory contains the nextflow working directories alongside the

Workflow outputs

The primary outputs of the workflow include:

  • a gzipped VCF file containing small variants found in the dataset.
  • an HTML report document detailing the primary findings of the workflow.

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