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.

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.