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 ]

input{:bash}

:file

BAM/CRAM/SAM/BCF/VCF/GVCF or jointly-called VCF file

input_index{:bash}

:file

index file of the input data, e.g., bam.bai, cram.crai

meta2{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘hg38’ ]

fasta{:bash}

:file

The reference fasta file

*.{fasta,fna,fas,fa}

meta3{:bash}

:map

Groovy Map containing reference information e.g. [ id:‘hg38’ ]

fai{:bash}

:file

FASTA index file

*.fai

meta4{:bash}

:map

Groovy Map containing sites information e.g. [ id:‘hg38’ ]

sites{:bash}

:file

sites file in VCF format which can be taken from https://github.com/brentp/somalier

*.vcf.gz

Output

name:type
description
pattern

extract{:bash}

meta{:bash}

:map

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

*.somalier{:bash}

:file

binary output file based on extracted sites

*.{somalier}

versions{:bash}

versions.yml{:bash}

: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 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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