split_into_chros.nf

Script to split a multi-chromosome VCF into single-chromosome VCFs

Dependencies

• bcftools

Nextflow workflow

This workflow is implemented in the script named split_into_chros.nf

Usage

nextflow run split_into_chros.nf --vcf input.vcf --chr chr20,chr21

Parameters

--vcf

The input VCF containing multiple chromosomes.

--prefix PREFIX

String used for output files. Default: 'out'

--outdir DIRNAME

Name of output dir. Default: 'outdir'

--chros LIST_OF_CHROS

Comma-separated list of chromosomes to generate. i.e. chr1,chr2,...

--cpus INT

Number of CPUs to use. Default 1

Output

The single-chrom VCFs will be put in the directory set by the params.outdir parameter. A tabix index per VCF will be also created