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Somalier

Supported Tool

Somalier does fast genotype :: pedigree correspondence checks from BAM/CRAM/VCF

Description

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 use for general QC.

File search patterns

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