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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

extract (file)

binary output file based on extracted sites

*.{somalier}
maintainers
Github user ashotmarg
Github user nvnieuwk
get in touch
Ask a question on Slack Open an issue on GitHub

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