Description

Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

extract (file(s))

extract file(s) from Somalier extract

*.somalier

ped (file)

optional path to a ped or fam file indicating the expected relationships among samples

*.{ped,fam}

sample_groups (file)

optional path to expected groups of samples such as tumor normal pairs specified as comma-separated groups per line

*.{txt,csv}

Output

Name (Type)
Description
Pattern

versions (file)

File containing software versions

versions.yml

html (file)

html file

*.html

pairs_tsv (file)

tsv file with output stats for pairs of samples

*.pairs.tsv

samples_tsv (file)

tsv file with sample-level information

*.samples.tsv
authors
Github user ashotmarg Github user nvnieuwk
get in touch
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Tools

somalier
MIT License

Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs

github.com/brentp/somalier github.com/brentp/somalier/blob/master/README.md https://github.com/brentp/somalier 10.1186/s13073-020-00761-2