Description

Correct UMIs in a BAM file to a fixed set of known UMIs with fgumi

Input

Name
Description
Pattern

0 ()

1 ()

umis (file)

Optional file(s) of known UMI sequences, passed to fgumi correct via --umi-files. Additional UMIs may be supplied inline with --umis via task.ext.args. Provide an empty list ([]) to rely on --umis.

*.txt

min_distance (integer)

Minimum required difference in mismatches between the best and second-best matching known UMI for a correction to be made (--min-distance).

keep_rejected (boolean)

If true, write reads whose UMIs could not be corrected to a separate rejects BAM file.

Output

Name
Description
Pattern

0 ()

0 ()

0 ()

0 ()

Tools

fgumi Documentation

High-performance tools for UMI-tagged sequencing data.

https://github.com/fulcrumgenomics/fgumiLicense: MIT
Authors