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:false ]

bam:file

BAM file contained mapped reads

meta2:map

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

bai:file

BAM file index

meta3:map

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

snp_bed:file

BED file containing SNP information (optional)

meta4:map

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

fasta:file

Input genome fasta file

meta5:map

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

index:directory

Directory containing biscuit genome index

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 (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
maintainers
Github user njspix
Github user sateeshperi
get in touch
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