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broadinstitute / ukbb_qc

QCing the UKBB
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Release HT update #212

Closed ch-kr closed 3 years ago

ch-kr commented 3 years ago

Added code to overwrite release HT to homalt branch. Only script to be reviewed is release/prepare_internal_data_release.py

ch-kr commented 3 years ago

I also edited get_freq_impacted_var and some code under if args.join_var in release/get_impacted_variants.py

ch-kr commented 3 years ago

that would work too (adjusting sex ploidies and checking for sites that wouldn't get adjusted). I wrote the code this way since this is how I found the extra sites during the sanity checks. should I change it?

ch-kr commented 3 years ago

I updated the code since your suggestion seems more straightforward

ch-kr commented 3 years ago

Closing this because patch has been released and we do not currently have plans to update the frequencies on the internal release HT