Enhance Sample and Variant-level QC

[smlmbrt]

Filters to implement:

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

  • Making sure it's properly read by plink with the VCF
  • [x] 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:

• Filters to restrict to autosomes and sex chromosomes as the current pipeline does not allow patches or non-standard names (ex. https://github.com/PGScatalog/pgsc_calc/issues/35#issuecomment-1204947083)

[smlmbrt]

Adding #14 to this issue.

[smlmbrt]

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

[smlmbrt]

Linking #149