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:map

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

]

bam:file

Biscuit BAM file

bai:file

BAM index

snp_bed:file

BED file containing SNP information (optional)

index:directory

Biscuit genome index directory (generated with ‘biscuit index’)

BiscuitIndex

Output

name:type
description
pattern

epiread_bed

meta:map

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

]

*.bed.gz:file

Gzipped BED file with methylation (and optionally SNV) information

*.{epiread.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/epiread_format https://github.com/huishenlab/biscuit
maintainer
Github user njspix
get in touch
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