github.com/johnpshelley/agd_genotypeconcordance/ExtractSubset_AGD

Automatic Tools and Workflows
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Task 1: Calculate genotype concordance

Steps:

  1. MEGA data needs to be lifted over to hg38 first!
  2. concordance_prepfiles.ipynb: Identify GRIDs and autosomal variants (CHR:POS) genotyped in the MEGA dataset (biovu_megaex_20231001_v2_plink_hg38)
  3. VUMC_CalculateGenotypeConcordance WDL: Extract the GRIDs and variants genotyped in MEGA. SNPs are mapped to hg38 and SNP IDs renamed as “CHR:POS:REF:ALT”. Multi-allelic variants, rare (MAF<1%), and variants with high missingness (>1
This is a companion discussion topic for the original entry at github.com/johnpshelley/agd_genotypeconcordance/ExtractSubset_AGD