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Add variant QC pipeline functions from gnomad_qc code #224

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Merged
jkgoodrich merged 13 commits into from
Jun 4, 2020
Merged

Add variant QC pipeline functions from gnomad_qc code #224

jkgoodrich merged 13 commits into from
Jun 4, 2020

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@jkgoodrich
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@jkgoodrich jkgoodrich commented May 12, 2020 •
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This PR is a bit big, but most of it is generalizing or adding functions from gnomad_qc that we will also be using in other pipelines

@jkgoodrich jkgoodrich requested review from ch-kr and lfrancioli May 12, 2020 16:01
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ch-kr requested changes May 20, 2020
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just a few small comments

lfrancioli
lfrancioli suggested changes May 26, 2020
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Thanks so much Julia for taking this on! Quite a few comments, many of which are really due to hail (and our usage of it) having evolved a lot since this was written!

@jkgoodrich jkgoodrich requested review from ch-kr and lfrancioli June 3, 2020 17:46
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lfrancioli reviewed Jun 3, 2020
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Fantastic work @jkgoodrich ! Just a few additional suggestions and nit-picks and it's good to go :)

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lfrancioli commented Jun 3, 2020

One more thing, seems like we've lost generate_final_rf_ht in the process -- was this on purpose?

jkgoodrich
jkgoodrich commented Jun 3, 2020
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Yeah I removed generate_final_rf_ht intentionally #224 (comment)

@jkgoodrich jkgoodrich requested a review from lfrancioli June 3, 2020 20:00
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ch-kr reviewed Jun 4, 2020
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one small comment and question

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lfrancioli commented Jun 4, 2020

Yeah I removed generate_final_rf_ht intentionally #224 (comment)

All right. Let's revisit once we have a plan for the finalization script in general.

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lfrancioli approved these changes Jun 4, 2020
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Looks great, good to go in my opinion :)

@jkgoodrich jkgoodrich merged commit 17bb157 into master Jun 4, 2020
@jkgoodrich jkgoodrich deleted the add_variantqc_pipeline_functions branch October 27, 2021 17:46
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@ch-kr ch-kr ch-kr approved these changes

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@lfrancioli lfrancioli lfrancioli approved these changes

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@jkgoodrich @lfrancioli @ch-kr