Tools for working with genomic and high throughput sequencing data.
Group: Unique Molecular Identifiers (UMIs)
Copies the UMI at the end of the BAM’s read name to the RX tag.
The read name is split on : characters with the last field is assumed to be the UMI sequence. The UMI
will be copied to the RX tag as per the SAM specification. If any read does not have a UMI composed of
valid bases (ACGTN), the program will report the error and fail.
If a read name contains multiple UMIs they may be delimited by either hyphens (-) or pluses (+). The
resulting UMI in the RX tag will always be hyphen delimited.
| Name | Flag | Type | Description | Required? | Max # of Values | Default Value(s) |
|---|---|---|---|---|---|---|
| input | i | PathToBam | The input BAM file | Required | 1 | |
| output | o | PathToBam | The output BAM file | Required | 1 | |
| remove-umi | Boolean | Remove the UMI from the read name | Optional | 1 | false |