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287 dynamically adjust minimum maf for hwe calculation and add option to set hwe p value threshold #300

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merged 3 commits into from
Jun 12, 2024
Merged

287 dynamically adjust minimum maf for hwe calculation and add option to set hwe p value threshold #300

merged 3 commits into from
Jun 12, 2024

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kliao12
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@kliao12 kliao12 commented Jun 10, 2024 •
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  • Create checkpoint that computes HWE maf to use for each population that meets criteria and writes to text file. HWE maf = min(config.hwe_maf, sqrt(5/n))
  • Rule plot_hwe reads in text file to define input/output wildcards for prior rule maf filtering
  • Updated docs to reflect changes

fix #287

@kliao12 kliao12 linked an issue Jun 10, 2024 that may be closed by this pull request
dynamically adjust minimum MAF for HWE calculation and add option to set HWE p value threshold #287
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@kliao12 kliao12 merged commit 719b6c0 into default Jun 12, 2024
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@kliao12 kliao12 deleted the 287-dynamically-adjust-minimum-maf-for-hwe-calculation-and-add-option-to-set-hwe-p-value-threshold branch June 12, 2024 19:00
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dynamically adjust minimum MAF for HWE calculation and add option to set HWE p value threshold
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