consensusreads

Calls consensus sequences from reads with the same unique molecular tag.

Quick Start

$ pbrun consensusreads \
    --ref Homo_sapiens_assembly38.fasta \
    --in-bam input.bam \
    --out-bam output.bam \
    --out-rejects-bam unused_reads.bam

consensusreads Reference

Calls consensus sequences from reads with the same unique molecular tag.

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 to write consensus reads. (default: None)

Option is required.

--out-rejects-bam OUT_REJECTS_BAM

Path of output BAM file to write reads not used. (default: None)

Option is required.

--ref REF

Path to the reference file. (default: None)

Option is required.

Options specific to this tool

--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)

--num-worker-threads NUM_WORKER_THREADS

Number of threads for worker (default 14) (default: 14)

--min-reads MIN_READS

The minimum number of reads to produce a consensus base (default 1) (default: 1)

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.