Somalier

Genotype to pedigree correspondence checks from sketches derived from BAM/CRAM or VCF

https://github.com/brentp/somalier

Somalier can be used to find sample swaps or duplicates in cancer projects, where there is often no jointly-called VCF across samples. It is also extremely efficient and so can be used to find all-vs-all relatedness estimates for thousands of samples. It also outputs information on sex, depth, heterozgyosity, and ancestry to be used for general QC.

File search patterns

somalier/pairs:
  contents: hom_concordance
  fn: "*.pairs.tsv"
  num_lines: 5
somalier/samples:
  contents: "#family_id"
  fn: "*.samples.tsv"
  num_lines: 5
somalier/somalier-ancestry:
  fn: "*.somalier-ancestry.tsv"