Comments (2)
Are there any updates on this issue? I believe I am having a similar problem in our implementation of the pipeline for GATK WGS.
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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)
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