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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

vcf (file)

Compressed VCF file

*.vcf.gz

tbi (file)

Index of the VCF file

*.vcf.gz.tbi
author
Github user nvnieuwk
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Tools

whamg
MIT

Structural variant detection and association testing

github.com/zeeev/wham 10.1371/journal.pcbi.1004572