WGS data

[jjfarrell]

The pipeline looks like it is optimized for processing imputed vcf data from UMICH or TOPMed imputation server which generates a DS field. Is is possible to run the pipeline on GATK WGS sequencing data without the DS field. Or does that need to be calculated with the PL field and written out to plink format before running the pipeline?

[aaleksandrov95]

Are there any updates on this issue? I believe I am having a similar problem in our implementation of the pipeline for GATK WGS.

[seppinho]

Hi,
I just double checked the Regenie repo, and regenie uses either DS or GT. So in case you want to use our pipeline, you have to convert it first (e.g. with plink2). If you have a working command, I'm happy to integrate that as a step into the pipeline. I think thats useful for many!

See here: rgcgithub/regenie#114 (comment)