UMI Options

Name

Description

Command Line Equivalent

Range

umi-library-type

Batch option for correcting UMIs.

--umi-library-type

Not required. The following are valid options: random-duplex / random-simplex / nonrandom-duplex

umi-enable

Enable UMI-based read processing.

--umi-enable

true / false

umi-correction-scheme

The methodology to use for correcting sequencing errors in UMIs.

--umi-correction-scheme

lookup / random / none / positional

umi-correction-table

Specify the correction table for lookup correction scheme.

--umi-correction-table

Path to table file

umi-emit-multiplicity

Consensus read output type.

--umi-emit-multiplicity

both/duplex/simplex

umi-min-supporting-reads

Number of input reads with matching UMI and position required to generate a consensus read.

--umi-min-supporting-reads

Integer ≥ 1. The default is 2.

umi-metrics-interval-file

Path to target regions file used for UMI on target metrics.

--umi-metrics-interval-file

Path to valid BED file

umi-source

The location to read UMIs from.

--umi-source

qname/bamtag/fastq

umi-fastq

Path to a separate FASTQ file with UMI sequences for each read

--umi-fastq

Path to valid FASTQ file

umi-nonrandom-whitelist

File listing valid nonrandom UMIs, one per line

--umi-nonrandom-whitelist

Path to file containing valid nonrandom UMI sequences

umi-fuzzy-window-size

Collapse reads with matching UMIs and alignment positions +/ this distance

--umi-fuzzy-window-size

Integer ≥ 1. The default is 3.