Description

Normalize VCF file

Input

name:type
description
pattern

meta:map

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

]

vcf:file

The vcf file to be normalized e.g. ‘file1.vcf’

*.{vcf,vcf.gz}

tbi:file

An optional index of the VCF file (for when the VCF is compressed)

*.vcf.gz.tbi

meta2:map

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

fasta:file

FASTA reference file

*.{fasta,fa}

Output

name:type
description
pattern

vcf

meta:map

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

]

*.{vcf,vcf.gz,bcf,bcf.gz}:file

One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file

*.{vcf,vcf.gz,bcf,bcf.gz}

tbi

meta:map

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

]

*.tbi:file

Alternative VCF file index

*.tbi

csi

meta:map

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

]

*.csi:file

Default VCF file index

*.csi

versions

versions.yml:file

File containing software versions

versions.yml