Description

Estimate repeat sizes using NGS data

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM/CRAM file

*.{bam,cram}

meta2 (map)

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

fasta (file)

Reference genome

*.{fna,fa,fasta}

meta3 (map)

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

fasta (file)

Reference genome index

*.fai

meta4 (map)

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

variant_catalog (file)

JSON file with repeat expansion sites to genotype

*.json

Output

Name (Type)
Description
Pattern

meta (map)

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

versions (file)

File containing software versions

versions.yml

vcf (file)

VCF with repeat expansions

*.vcf.gz

json (file)

JSON with repeat expansions

*.json.gz
included in
raredisease
author
Github user jemten
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