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302 skip merging graf king and plink results to make the qc pipeline more efficient #310

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kliao12
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@kliao12 kliao12 commented Aug 5, 2024

Removed merging graf/king results in sample_concordance.py to speed up computation time with large samples. Removed logic that uses graf/king results for concordance checks (replicates) and only uses plink now.

Fixes #302

@kliao12 kliao12 merged commit 3d31024 into default Aug 6, 2024
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@kliao12 kliao12 deleted the 302-skip-merging-graf-king-and-plink-results-to-make-the-qc-pipeline-more-efficient branch August 6, 2024 17:43
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kliao12 commented Aug 8, 2024

For 90k sample set reduces rule sample_concordance_summary from 1 day 4 hours to 15 hours. Removing graf/king information when checking for discordant/unexpected replicates does not change counts in table 4a or 4b

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skip merging Graf, King and Plink results to make the QC pipeline more efficient
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