Find ligation junctions in .sam, make .pairs
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam:file
BAM/CRAM/SAM file
*.{bam,cram,sam}
chromsizes:file
chromosome size file
pairsam
*.pairsam.gz:file
parsed pair file
*.{pairsam.gz}
stat
*.pairsam.stat:file
stats of the pairs
*.{pairsam.stat}
versions
versions.yml:file
File containing software versions
versions.yml
CLI tools to process mapped Hi-C data
