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{:bash}

:map

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

bam{:bash}

:file

BAM/SAM file

*.{bam,sam}

bai{:bash}

:file

BAM index file

*.bai

fasta{:bash}

:file

Reference Fasta file

*.{fasta,fa}

fasta_fai{:bash}

:file

Index of the reference Fasta

*.fai

Output

name:type
description
pattern

vcf{:bash}

meta{:bash}

:map

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

*.vcf.gz{:bash}

:file

Compressed VCF file

*.vcf.gz

tbi{:bash}

meta{:bash}

:map

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

*.vcf.gz.tbi{:bash}

:file

Index of the VCF file

*.vcf.gz.tbi

graph{:bash}

meta{:bash}

:map

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

*.txt{:bash}

:file

Graph file

*.txt

versions{:bash}

versions.yml{:bash}

: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
Ask a question on Slack Open an issue on GitHub