Workflow to calculate DS with Hail

Workflow uses Hail: Hail Team. Hail 0.2.131-11d9b2ff89da.

Usage examples

Running the workflow

nextflow run main.nf -resume

Pipeline should create the following files in your working directory:

work            # Directory containing the nextflow working files
{outdir}/concatenated_vcf/         # Concatenated VCF file with DS field 

Info needed in nextflow.config file

All VCF files must have the same sample columns appearing in the same order (workflow uses bcftools concat).

• autosomal_PAR_vcf : path to the VCF file containing autosomal chromosomes and the chrX PAR region with GT field
• non_PAR_vcf : path to the VCF file containing the chrX non-PAR region without structural variants with GT field
• metadata : path to the metadata file containing columns genotype_id and sex. The sex column must exclusively contain values female and male.
• concated_vcf_file_name : output VCF.gz file name
• outdir : output path