Description

The wham suite consists of two programs, wham and whamg. wham, the original tool, is a very sensitive method with a high false discovery rate. The second program, whamg, is more accurate and better suited for general structural variant (SV) discovery.

Input

name:type
description
pattern

meta:map

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

]

bam:file

BAM/SAM file

*.{bam,sam}

bai:file

BAM index file

*.bai

fasta:file

Reference Fasta file

*.{fasta,fa}

fasta_fai:file

Index of the reference Fasta

*.fai

Output

name:type
description
pattern

vcf

meta:map

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

]

*.vcf.gz:file

Compressed VCF file

*.vcf.gz

tbi

meta:map

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

]

*.vcf.gz.tbi:file

Index of the VCF file

*.vcf.gz.tbi

graph

meta:map

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

]

*.txt:file

Graph file

*.txt

versions

versions.yml:file

File containing software versions

versions.yml

Tools

whamg
MIT

Structural variant detection and association testing

github.com/zeeev/wham 10.1371/journal.pcbi.1004572
maintainer
Github user nvnieuwk
get in touch
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