GATK Variant calling pipeline for genomic data using Nextflow
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
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.
The input files required to run the pipeline:
- Genomic sequence paired reads,
*_{1,2}.fq.gz - Reference genome,
*.fa
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'
- 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'
- 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
- The path to the directory for the output files.
- Default parameter:
$projectDir/output