Description

The Java port of the VarDict variant caller

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bams (file)

One or two BAM files. Supply two BAM files to run Vardict in paired mode.

*.bam

bais (file)

Index/indices of the BAM file(s)

*.bai

bed (file)

BED with the regions of interest

*.bed

meta2 (map)

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

]

fasta (file)

FASTA of the reference genome

*.{fa,fasta}

meta3 (map)

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

]

fasta_fai (file)

The index of the FASTA of the reference genome

*.fai

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

vcf (file)

VCF file output

*.vcf.gz

Tools

vardictjava
MIT

Java port of the VarDict variant discovery program