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