Tools for working with genomic and high throughput sequencing data.
Group: SAM/BAM
Randomizes the order of reads in a SAM or BAM file. Randomization is done by sorting
on a hash of the queryname (and bases and quals if not query-grouping). By default
reads with the same query name are grouped together in the output file; this can be
turned off by specifying –query-group=false.
| Name | Flag | Type | Description | Required? | Max # of Values | Default Value(s) |
|---|---|---|---|---|---|---|
| input | i | PathToBam | The input SAM or BAM file. | Optional | 1 | /dev/stdin |
| output | o | PathToBam | The output SAM or BAM file. | Optional | 1 | /dev/stdout |
| seed | s | Int | Random seed. | Optional | 1 | 42 |
| query-group | q | Boolean | Group together reads by queryname. | Optional | 1 | true |