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broadinstitute / gnomad_local_ancestry

Hail batch pipeline and scripts for local ancestry inference
MIT License
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Add VCF generation #95

Closed mike-w-wilson closed 3 years ago

mike-w-wilson commented 3 years ago

These additions allow the user to generate a VCF from Tractor's output files with ancestral AC, AN, and AF annotations. It also adds groupings to the args.

mike-w-wilson commented 3 years ago

Also I tried researching msp and could not find it either, based on the wording around the ouput in the RFMix manual it may be something along the lines or most likely subpopulations?

mike-w-wilson commented 3 years ago

Back to you @ch-kr ! I added newlines lines around all the commands because I think isolating them makes them more readable but if you disagree, I can change them back. That single character makes the difference on the black format of the lai_input function 🤷 .