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 ]

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}

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}

Output

name:type
description
pattern

tsv

meta:map

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

*-ancestry.tsv:file

TSV with ancestry information for query and labelled samples.

*.{-ancestry.tsv}

html

meta:map

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

*-ancestry.html:file

html file with ancestry information for query and labelled samples.

*.{-ancestry.html}

versions

versions.yml:file

File containing software versions

versions.yml

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 10.1186/s13073-020-00761-2
Github user atrigila
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