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}

bai:file

Index of BAM/CRAM file

*.{bai,crai}

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_fai: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

vcf

meta:map

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

*.vcf.gz:file

VCF with repeat expansions

*.vcf.gz

json

meta:map

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

*.json.gz:file

JSON with repeat expansions

*.json.gz

bam

meta:map

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

*_realigned.bam:file

BAM/CRAM file

*.{bam,cram}

versions

versions.yml:file

File containing software versions

versions.yml