Quick start

If you have not already done so, install kevlar using the following instructions, and Snakemake version 5.0 or greater.

The simplest way to execute kevlar’s entire de novo variant discovery workflow is using the provided Snakemake workflow configuration. Processing the example data set below should be able to run on a laptop in less than 5 minutes while consuming less than 200 Mb of RAM. The results (workdir/calls.scored.sorted.vcf.gz) should include 5 variant calls: a 300 bp insertion and 4 single-nucleotide variants.

A more detailed tutorial is available, and a complete listing of all available configuration options for each kevlar command can be found in the CLI documentation, or by executing kevlar <subcommand> -h in the terminal.

# Download data
curl -L https://s3-us-west-1.amazonaws.com/noble-trios/helium-mother-reads.fq.gz -o mother.fq.gz
curl -L https://s3-us-west-1.amazonaws.com/noble-trios/helium-father-reads.fq.gz -o father.fq.gz
curl -L https://s3-us-west-1.amazonaws.com/noble-trios/helium-proband-reads.fq.gz -o proband.fq.gz
curl -L https://s3-us-west-1.amazonaws.com/noble-trios/helium-refr.fa.gz -o refr.fa.gz
bwa index refr.fa.gz

# Download and format configuration file
curl -L https://s3-us-west-1.amazonaws.com/noble-trios/helium-config.json \
    | sed "s:/home/user/Desktop:$(pwd):g" > helium-config.json

# Invoke the workflow
snakemake \
    --snakefile kevlar/workflows/mark-I/Snakefile \
    --configfile helium-config.json --cores 4 --directory workdir -p calls