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{:bash}

:map

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

extract{:bash}

:file

extract file(s) from Somalier extract

*.somalier

ped{:bash}

:file

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

*.{ped,fam}

sample_groups{:bash}

: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

html{:bash}

meta{:bash}

:file

html file

*.html

*.html{:bash}

:file

html file

*.html

pairs_tsv{:bash}

meta{:bash}

:file

html file

*.html

*.pairs.tsv{:bash}

:file

tsv file with output stats for pairs of samples

*.pairs.tsv

samples_tsv{:bash}

meta{:bash}

:file

html file

*.html

*.samples.tsv{:bash}

:file

tsv file with sample-level information

*.samples.tsv

versions_somalier{:bash}

${task.process}{:bash}

:string

The name of the process

somalier{:bash}

:string

The name of the tool

somalier 2>&1 | sed -n 's/.*version: \([0-9.]*\).*/\1/p'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

somalier{:bash}

:string

The name of the tool

somalier 2>&1 | sed -n 's/.*version: \([0-9.]*\).*/\1/p'{:bash}

:eval

The expression to obtain the version of the tool

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
maintainers
Github user ashotmarg
Github user nvnieuwk
get in touch
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