Whole-genome sequencing pipeline

Pipeline for the alignment, variant calling, copy number calling and annotation of whole-genome sequencing data, built on top of the sarek Nextflow pipeline. Please refer to its documentation for details.

Usage

run_wgs_pipeline.sh [-g|--genome <arg>] [-h|--help] [--version] <samplesheet> <outdir>
    <samplesheet>: path to the samplesheet CSV file
    <outdir>: path to the output directory where to store the results
    -g, --genome: genome to be used (default: 'GATK.GRCh37')
    -h, --help: Prints help
    --version: Prints version

where

• samplesheet is a CSV file
• outdir is the path where the results will be stored
• genome is the reference genome to be used

For example:

run_wgs_pipeline.sh --genome GRCm38 design.csv wgs

will run the pipeline on the samples specified in the design.csv file, will store the results in the wgs folder, and will align the reads to the GRCm38 genome.

Structure of the sample sheet

Check the sarek documentation about the required input.

An example input file is provided: test_input.csv.

Available genomes

Homo sapiens

• GATK.GRCh37 (from Broad Institute)

Mus musculus

• GRCm38 (from Ensembl)