modules/biscuit_vcf2bed

Summarizes methylation or SNV information from a Biscuit VCF in a standard-compliant BED file.

biscuitDNA methylationWGBSscWGBSbisulfite sequencingalignervcf

https://github.com/nf-core/modules/[...]/modules/nf-core/biscuit/vcf2bed

Description

Summarizes methylation or SNV information from a Biscuit VCF in a standard-compliant BED file.

Input

name:type

description

pattern

`meta:map`

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

`vcf:file`

Biscuit vcf file (output of biscuit pileup)

Output

name:type

description

pattern

`bed`

`meta:map`

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

`*.bed.gz:file`

Gzipped BED file with methylation or SNV information

*.{bed.gz}

`versions`

`versions.yml:file`

File containing software versions

versions.yml

Tools

biscuit
MIT

A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data

huishenlab.github.io/biscuit huishenlab.github.io/biscuit/docs/methylextraction https://github.com/huishenlab/biscuit

modules/biscuit_vcf2bed

Description

Input

meta:map

vcf:file

Output

bed

meta:map

*.bed.gz:file

versions

versions.yml:file

Tools

biscuit MIT

`meta:map`

`vcf:file`

`bed`

`meta:map`

`*.bed.gz:file`

`versions`

`versions.yml:file`

biscuit
MIT