Peddy

Compares familial-relationships and sexes as reported in a PED file with those inferred from a VCF

https://github.com/brentp/peddy

It samples the VCF at about 25000 sites (plus chrX) to accurately estimate relatedness, IBS0, heterozygosity, sex and ancestry. It uses 2504 thousand genome samples as backgrounds to calibrate the relatedness calculation and to make ancestry predictions. It does this very quickly by sampling, by using C for computationally intensive parts, and parallelization.

File search patterns

peddy/background_pca:
  fn: "*.background_pca.json"
peddy/het_check:
  fn: "*.het_check.csv"
peddy/ped_check:
  fn: "*.ped_check.csv"
peddy/sex_check:
  fn: "*.sex_check.csv"
peddy/summary_table:
  fn: "*.peddy.ped"