Command-line options

The vip command takes input vcf/cram/fastq data and produces a filtered annotated .vcf.gz containing candidate variants of interest.

In addition to the .vcf.gz an interactive .html report is produced that can be displayed in any modern web browser.

vip --help prints the available command-line options: 

usage: vip -w <arg> -i <arg> -o <arg>
  -w, --workflow <arg>  workflow to execute. allowed values: cram, fastq, gvcf, vcf
  -i, --input    <arg>  path to sample sheet .tsv
  -o, --output   <arg>  output folder
  -c, --config   <arg>  path to additional nextflow .cfg (optional)
  -p, --profile  <arg>  nextflow configuration profile (optional)
  -r, --resume          resume execution using cached results (default: false)
  -h, --help            print this message and exit

Required

  • workflow as described here
  • input as described here
  • output as described here

Optional

  • config as described here
  • profile the configuration profile to use. allowed values are local, slurm plus any profiles added in --config
  • resume useful to continue executions that was stopped by an error using cached results

Defaults

By default vip:

  • Assumes an Illumina sequencing platform was used to generate the input data
  • Assumes whole-genome sequencing (WGS) method was used to generate the input data
  • Uses a GRCh38 reference genome (GCA_000001405.15 / GCF_000001405.26)
  • Provides classification trees for default variant filtration. For details, see here
  • Creates reports using a default report template. For details, see here