Description

Groups reads together that appear to have come from the same original molecule. Reads are grouped by template, and then templates are sorted by the 5’ mapping positions of the reads from the template, used from earliest mapping position to latest. Reads that have the same end positions are then sub-grouped by UMI sequence. (!) Note: the MQ tag is required on reads with mapped mates (!) This can be added using samblaster with the optional argument —addMateTags.

Input

Name (Type)
Description
Pattern

meta (map)

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

]

bam (file)

BAM file. Note: the MQ tag is required on reads with mapped mates (!)

*.bam

strategy (value)

Reguired argument: defines the UMI assignment strategy.
Must be chosen among: Identity, Edit, Adjacency, Paired.

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

bam (file)

UMI-grouped BAM

*.bam

histogram (file)

A text file containing the tag family size counts

*.txt

Tools

fgbio
MIT

A set of tools for working with genomic and high throughput sequencing data, including UMIs