Adds and/or fixes mate information on paired-end reads.


$ pbrun setmateinfo \ --in-bam sorted_or_grouped_input.bam \ --out-bam output.bam

Adds and/or fixes mate information on paired-end reads.

Input/Output file options

--in-bam IN_BAM

Path to the input BAM 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). (default: None)

Option is required.

--out-bam OUT_BAM

Path of the output BAM file. (default: None)

Option is required.

Options specific to this tool


Common options:

--logfile LOGFILE

Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)

--tmp-dir TMP_DIR

Full path to the directory where temporary files will be stored.

--with-petagene-dir WITH_PETAGENE_DIR

Full path to the PetaGene installation directory. By default, this should have been installed at /opt/petagene. Use of this option also requires that the PetaLink library has been preloaded by setting the LD_PRELOAD environment variable. Optionally set the PETASUITE_REFPATH and PGCLOUD_CREDPATH environment variables that are used for data and credentials (default: None)


Do not delete the directory storing temporary files after completion.

--license-file LICENSE_FILE

Path to license file license.bin if not in the installation directory.


Do not override seccomp options for docker (default: None).


View compatible software versions.

© Copyright 2023, Nvidia. Last updated on Jun 28, 2023.