Description

Calls consensus sequences from reads with the same unique molecular tag.

Input

name:type
description
pattern

meta:map

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

, collapse
]

grouped_bam:file

The input SAM or BAM file, grouped by UMIs

*.{bam,sam}

min_reads:integer

Minimum number of original reads to build each consensus read.

min_baseq:integer

Ignore bases in raw reads that have Q below this value.

Output

name:type
description
pattern

bam

meta:map

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

]

*.bam:file

Output SAM or BAM file to write consensus reads.

*.{bam,sam}

versions

versions.yml:file

File containing software versions

versions.yml

Tools

fgbio
MIT

Tools for working with genomic and high throughput sequencing data.