Groups reads together that appear to have come from the same original molecule.
$ pbrun groupreadsbyumi \
--ref Homo_sapiens_assembly38.fasta \
--in-bam input.bam \
--out-bam output.bam
Groups reads together that appear to have come from the same original molecule.
Input/Output file options
- --in-bam IN_BAM
-
Path to the input BAM file. (default: None)
Option is required.
- --out-bam OUT_BAM
-
Path of output BAM file after grouping reads. (default: None)
Option is required.
- --ref REF
-
Path to the reference file. (default: None)
Option is required.
Options specific to this tool
- --strategy STRATEGY
-
The UMI assignment strategy: adjacency or paired. (default: )
Option is required.
- --num-zip-threads NUM_ZIP_THREADS
-
Number of CPUs to use for zipping bam files in a run (default 16 for coordinate sorts and 10 otherwise) (default: None)
- --num-sort-threads NUM_SORT_THREADS
-
Number of CPUs to use for sorting in a run (default 10 for coordinate sorts and 16 otherwise) (default: None)
- --max-records-in-ram MAX_RECORDS_IN_RAM
-
Maximum number of records in RAM when using a queryname or template coordinate sort mode; lowering this number will decrease maximum memory usage. (default: 65000000)
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)
- --keep-tmp
-
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.
- --no-seccomp-override
-
Do not override seccomp options for docker (default: None).
- --version
-
View compatible software versions.