Description

converts sam/bam/cram/pairs into genome contact map

Input

Name (Type)
Description
Pattern

meta (map)

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

]

input (file)

BAM/CRAM/SAM file or pairs formatted reads file

*.{bam,cram,sam,pairs.gz}

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

pretext (file)

pretext map

*.pretext
authors
Github user marrip Github user getrudeln
get in touch
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Tools

pretextmap
MIT

Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps.

github.com/wtsi-hpag/PretextMap github.com/wtsi-hpag/PretextMap/blob/master/README.md