Calls consensus sequences from reads with the same double-stranded source molecule.

Prior to running this tool, reads must be grouped by UMI (see groupreadsbyumi).

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\$ pbrun duplexconsensusreads \
--ref theReferenceFile.fasta \
--in-bam theInputBam.bam \
--out-bam theOutputBam.bam


Calls consensus sequences from reads with the same double-stranded source 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 to write consensus reads. (default: None)

Option is required.

--ref REF

Path to the reference file. (default: None)

Option is required.

### Pipeline Options:

Number of CPUs to use for zipping BAM files in a run (default 16 for coordinate sorts and 10 otherwise). (default: None)

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)

Number of threads for worker. (default: 14)

--error-rate-pre-umi ERROR_RATE_PRE_UMI

The Phred-scaled error rate for an error prior to the UMIs being integrated. (default: 45)

--error-rate-post-umi ERROR_RATE_POST_UMI

The Phred-scaled error rate for an error post the UMIs have been integrated. (default: 40)

--min-input-base-quality MIN_INPUT_BASE_QUALITY

Ignore bases in raw reads that have Q below this value. (default: 10)

The minimum number of reads to produce a consensus base. This option can take 1-3 values. f fewer than three values are supplied, the last value is repeated (i.e. 5 4 -> 5 4 4 and 1 -> 1 1 1. The first value applies to the final consensus read, the second value to one single-strand consensus, and the last value to the other single-strand consensus. It is required that if values two and three differ, the more stringent value comes earlier. (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.