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

meta (map)

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

]

versions (file)

File containing software versions

versions.yml

pairsam (file)

parsed pair file

*.{pairsam.gz}

stat (file)

stats of the pairs

*.{pairsam.stat}
included in
hicar
maintainer
Github user jianhong
get in touch
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Tools

pairtools
MIT

CLI tools to process mapped Hi-C data

http://pairtools.readthedocs.io https://github.com/mirnylab/pairtools