github.com/johnpshelley/agd_genotypeconcordance/PLINK_SexCheck

Automatic Tools and Workflows
1

Calculate genotype concordance

Steps:

  1. JS_GetMEGAVariants.ipynb: Identify GRIDs and autosomal variants (CHR:POS) genotyped in MEGA dataset (biovu_megaex_20231001_v2_plink_hg38)
  2. VUMC_CalculateGenotypeConcordance WDL: Extract from AGD the GRIDs and variants genotyped in MEGA. SNPs are mapped to hg38 and SNP IDs renamed according to CHR:POS:REF:ALT. Multi-allelic variants were also excluded. Missingness and allele frequency for each variant is also calculated.
  3. **VUMC_Calcu
This is a companion discussion topic for the original entry at github.com/johnpshelley/agd_genotypeconcordance/PLINK_SexCheck