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

meta (map)

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

]

epiread_bed (file)

Gzipped BED file with methylation (and optionally SNV) information

*.{epiread.bed.gz}

versions (file)

File containing software versions

versions.yml
maintainer
Github user njspix
get in touch
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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