modules/whamg

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.

whamgwhamvcfbamvariant calling

https://github.com/nf-core/modules/[...]/modules/nf-core/whamg

Description

Input

name:type

description

pattern

`meta:map`

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

`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:false ]

`*.vcf.gz:file`

Compressed VCF file

*.vcf.gz

`tbi`

`meta:map`

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

`*.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:false ]

`*.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

modules/whamg

Description

Input

meta:map

bam:file

bai:file

fasta:file

fasta_fai:file

Output

vcf

meta:map

*.vcf.gz:file

tbi

meta:map

*.vcf.gz.tbi:file

graph

meta:map

*.txt:file

versions

versions.yml:file

Tools

whamg MIT

`meta:map`

`bam:file`

`bai:file`

`fasta:file`

`fasta_fai:file`

`vcf`

`meta:map`

`*.vcf.gz:file`

`tbi`

`meta:map`

`*.vcf.gz.tbi:file`

`graph`

`meta:map`

`*.txt:file`

`versions`

`versions.yml:file`

whamg
MIT