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:false ]

query_somalier_files (file)

Set of somalier files for query samples. Obtained via somalier extract.

*.{somalier}

meta2 (map)

Groovy Map containing labelled samples information
e.g. [ id:'test', single_end:false ]

labelled_somalier_files (file)

Set of somalier files for labelled samples. e.g. Somalier files for 1kg https://zenodo.org/record/3479773/files/1kg.somalier.tar.gz?download=1

*.{somalier}

labels_tsv (file)

TSV for labelled samples. e.g. Somalier labels for 1kg https://raw.githubusercontent.com/brentp/somalier/master/scripts/ancestry-labels-1kg.tsv

*.{tsv}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

versions (file)

File containing software versions

versions.yml

tsv (file)

TSV with ancestry information for query and labelled samples.

*.{-ancestry.tsv}

html (file)

html file with ancestry information for query and labelled samples.

*.{-ancestry.html}
author
Github user atrigila
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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/somalier10.1186/s13073-020-00761-2