groupreadsbyumi

Groups reads together that appear to have come from the same original molecule.

Quick Start

$ pbrun groupreadsbyumi \
    --ref Homo_sapiens_assembly38.fasta \
    --in-bam input.bam \
    --out-bam output.bam

groupreadsbyumi Reference

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 the output BAM file after grouping reads. (default: None)

Option is required.

--ref REF

Path to the reference file. (default: None)

Option is required.

Pipeline Options:

--strategy STRATEGY

The UMI assignment strategy, which can be adjacency or paired. (default: )

Option is required.

--min-map-q MIN_MAP_Q

Minimum mapping quality. (default: 30)

--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.