Description

Call structural variants

Input

Name (Type)
Description
Pattern

meta (map)

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

]

input (file)

BAM/CRAM file from alignment must be sorted, indexed, and duplicate marked

*.{bam,cram}

input_index (file)

Index of the BAM/CRAM file

*.{bai,crai}

vcf (file)

A BCF/VCF file to genotype with Delly. If this is supplied, the variant calling will be skipped

*.{vcf.gz,bcf}

vcf_index (file)

The index of the BCF/VCF file

*.{tbi,csi}

exclude_bed (file)

An optional bed file containing regions to exclude from the called VCF

*.bed

meta2 (map)

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

]

fasta (file)

The reference fasta file

*.{fasta,fa}

meta3 (map)

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

]

fai (file)

Index of reference fasta file to identify split-reads

*.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

bcf (file)

Called variants in BCF/VCF format. Specify either “bcf” or “vcf” in ext.suffix to define the output type

*.{bcf,vcf.gz}

csi (file)

A generated csi index that matches the bcf output (not generated for vcf files)

*.{bcf.csi}

Tools

delly
BSD-3-Clause

Structural variant discovery by integrated paired-end and split-read analysis