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