BCCDC-PHL / call-variants

Align against a reference genome and call variants

Call Variants Pipeline

This pipeline takes a directory containing paired-end illumina sequence data, plus a reference sequence, aligns the reads against the reference and calls variants. It is based directly off of the excellent Snippy by Torsten Seemann (@tseemann).

Usage

nextflow run BCCDC-PHL/call-variants \
  --ref <ref.fa> \
  --gff <genes.gff> \
  --fastq_input </path/to/fastq> \
  --outdir <outdir>