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

fasta (file)

The reference fasta file

*.{fasta,fna,fas,fa}

fai (file)

FASTA index file

*.fai

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}
authors
Github user ashotmarg Github user nvnieuwk
get in touch
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Tools

somalier
MIT License

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