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primed-bcftools

This repository contains WDLs for using bcftools on AnVIL for the PRIMED consortium.

extract_vcf_ids

This workflow uses [bcftools query] to extract variant identifiers with the form of CHR:POS:REF:ALT from a set of VCFs.

Inputs:

input description
vcf_file Array of vcf files to extract ids from
pass_only Boolean indicator of whether only pass variants should be included, using FILTER=PASS.

Outputs:

output description
variant_file File containing the extracted variant ids, one per line