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 the following command:

nextflow run jdetras/snp-calling -r main -profile docker

Pipeline Description

The variant calling pipeline follows the recommended practices from GATK. The input genomic data are aligned to a reference genome using BWA. The alignemnt files are processed using Picard Tools. Variant calling is done using samtools and GATK.

Input files

The input files required to run the pipeline:

• Genomic sequence paired reads, *_{1,2}.fq.gz
• Reference genome, *.fa

Pipeline parameters

Usage

Usage: nextflow run jdetras/snp-calling -profile docker [options]

Options:

• --reads
• --genome
• --output

Example: $ nextflow run jdetras/snp-calling -profile docker --reads '/path/to/reads/*_{1,2}.fq.gz' --genome '/path/to/reference/genome.fa' --output '/path/to/output'

--reads

• The path to the FASTQ read files.
• Wildcards (*, ?) can be used to declare multiple reads. Use single quotes when wildcards are used.
• Default parameter: $projectDir/data/reads/*_{1,2}.fq.gz

Example: $ nextflow run jdetras/snp-calling -profile docker --reads '/path/to/reads/*_{1,2}.fq.gz'

--genome

• The path to the genome file in fasta format.
• The extension is .fa.
• Default parameter: $projectDir/data/reference/genome.fa

Example: $ nextflow run jdetras/snp-calling -profile docker --genome /path/to/reference/genome.fa

--output

• The path to the directory for the output files.
• Default parameter: $projectDir/output

Software

• BWA 0.7.17
• Samtools 1.3.1
• GATK 4.2.6.1