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Somalier

note

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'