Description

Summarizes read-level methylation (and optionally SNV) information from a Biscuit BAM file in a standard-compliant BED format.

Input

name:type
description
pattern

meta{:bash}

:map

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

bam{:bash}

:file

BAM file contained mapped reads

meta2{:bash}

:map

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

bai{:bash}

:file

BAM file index

meta3{:bash}

:map

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

snp_bed{:bash}

:file

BED file containing SNP information (optional)

meta4{:bash}

:map

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

fasta{:bash}

:file

Input genome fasta file

meta5{:bash}

:map

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

index{:bash}

:directory

Directory containing biscuit genome index

Output

name:type
description
pattern

bed{:bash}

meta{:bash}

:map

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

*.bed.gz{:bash}

:file

Gzipped BED file with methylation (and optionally SNV) information

*.{epiread.bed.gz}

versions_biscuit{:bash}

${task.process}{:bash}

:string

The name of the process

biscuit{:bash}

:string

The name of the tool

biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'{:bash}

:eval

The expression to obtain the version of the tool

versions_samtools{:bash}

${task.process}{:bash}

:string

The name of the process

samtools{:bash}

:string

The name of the tool

samtools --version |& sed '1!d; s/^.*samtools //'{:bash}

:eval

The expression to obtain the version of the tool

Topics

name:type
description
pattern

versions{:bash}

${task.process}{:bash}

:string

The name of the process

biscuit{:bash}

:string

The name of the tool

biscuit version |& sed '1!d; s/^.*BISCUIT Version: //'{:bash}

:eval

The expression to obtain the version of the tool

${task.process}{:bash}

:string

The name of the process

samtools{:bash}

:string

The name of the tool

samtools --version |& sed '1!d; s/^.*samtools //'{:bash}

:eval

The expression to obtain the version of the tool

Tools

biscuit
MIT

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

huishenlab.github.io/biscuit huishenlab.github.io/biscuit/epiread_format https://github.com/huishenlab/biscuit
maintainers
Github user njspix
Github user sateeshperi
get in touch
Ask a question on Slack Open an issue on GitHub