Description

Find ligation junctions in .sam, make .pairs

Input

name:type
description
pattern

meta:map

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

]

bam:file

BAM/CRAM/SAM file

*.{bam,cram,sam}

chromsizes:file

chromosome size file

Output

name:type
description
pattern

pairsam

meta:map

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

]

*.pairsam.gz:file

parsed pair file

*.{pairsam.gz}

stat

meta:map

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

]

*.pairsam.stat:file

stats of the pairs

*.{pairsam.stat}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

pairtools
MIT

CLI tools to process mapped Hi-C data