Tools for working with genomic and high throughput sequencing data.
Group: SAM/BAM
Adds and/or fixes mate information on paired-end reads. Sets the MQ (mate mapping quality),
MC (mate cigar string), ensures all mate-related flag fields are set correctly, and that
the mate reference and mate start position are correct.
Supplementary records are handled correctly (updated with their mate’s non-supplemental attributes). Secondary alignments are passed through but are not updated.
The input file must be query-name sorted or query-name grouped (i.e. all records from the same query sequence must be adjacent in the file, though the ordering between queries is unspecified).
| Name | Flag | Type | Description | Required? | Max # of Values | Default Value(s) |
|---|---|---|---|---|---|---|
| input | i | PathToBam | Input SAM/BAM/CRAM file. | Optional | 1 | /dev/stdin |
| output | o | PathToBam | Output SAM/BAM/CRAM file. | Optional | 1 | /dev/stdout |
| ref | r | PathToFasta | Reference fasta, only needed if writing CRAM. | Optional | 1 | |
| allow-missing-mates | x | Boolean | If specified, do not fail when reads marked as paired are missing their mate pairs. | Optional | 1 | false |