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Enhance Sample and Variant-level QC #21

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smlmbrt opened this issue Mar 21, 2022 · 3 comments
Open
1 task done

Enhance Sample and Variant-level QC #21

smlmbrt opened this issue Mar 21, 2022 · 3 comments
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enhancement New feature or request

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smlmbrt commented Mar 21, 2022 •
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Filters to implement:

  • Sex check based on the input/headers of genotyping-files

    • Making sure it's properly read by plink with the VCF
    • plink2 now throws error if sex isn't declared when sex-chromosomes are present in the input.

  • Genotyping inputs:

    • Duplicate variant checks (perhaps after re-labelling?)
    • Filters for (imputation quality, MAF, genotype missingness)

Consider implementing:
@smlmbrt smlmbrt added the enhancement New feature or request label Mar 21, 2022
@smlmbrt smlmbrt changed the title Sample-level QC Add Sample and Variant-level QC Apr 25, 2022
@smlmbrt smlmbrt changed the title Add Sample and Variant-level QC Add Sample and Variant-level QC Checks + Filters May 18, 2022
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smlmbrt commented Sep 1, 2022

Adding #14 to this issue.

@smlmbrt smlmbrt changed the title Add Sample and Variant-level QC Checks + Filters Sample and Variant-level QC Filters Sep 16, 2022
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smlmbrt commented Jan 16, 2023

Linking #74 to this issue. Plan to implement stricter input checks

@smlmbrt smlmbrt changed the title Sample and Variant-level QC Filters Enhance Sample and Variant-level QC Jan 16, 2023
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smlmbrt commented Aug 10, 2023

Linking #149

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