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. |