SNP-Calling

GATK Variant calling pipeline for genomic data using Nextflow

Quickstart

Install Nextflow using the following command:

curl -s https://get.nextflow.io | bash

Index reference genome:

$ bwa index /path/to/reference/genome.fa

$ samtools faidx /path/to/reference/genome.fa

$ gatk CreateSequenceDictionary -R /path/to/genome.fa -O genome.dict

Launch the pipeline execution with ...