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)

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
maintainers
Github user ashotmarg
Github user nvnieuwk
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

somalier
MIT

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