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

]

input:file

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

input_index:file

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

meta2:map

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

fasta:file

The reference fasta file

*.{fasta,fna,fas,fa}

meta3:map

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

fai:file

FASTA index file

*.fai

meta4:map

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

sites:file

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

*.vcf.gz

Output

name:type
description
pattern

extract

meta:map

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

]

*.somalier:file

binary output file based on extracted sites

*.{somalier}

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 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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