consensusreads
Calls consensus sequences from reads with the same unique molecular tag.
$ pbrun consensusreads \
--ref Homo_sapiens_assembly38.fasta \
--in-bam input.bam \
--out-bam output.bam \
--out-rejects-bam unused_reads.bam
Calls consensus sequences from reads with the same unique molecular tag.
Input/Output file options
- --in-bam IN_BAM
- --out-bam OUT_BAM
- --out-rejects-bam OUT_REJECTS_BAM
- --ref REF
Path to the input BAM file. (default: None)
Option is required.
Path of the output BAM file to write consensus reads. (default: None)
Option is required.
Path of the output BAM file to write reads not used. (default: None)
Option is required.
Path to the reference file. (default: None)
Option is required.
Pipeline Options:
- --num-zip-threads NUM_ZIP_THREADS
- --num-sort-threads NUM_SORT_THREADS
- --max-records-in-ram MAX_RECORDS_IN_RAM
- --num-worker-threads NUM_WORKER_THREADS
- --error-rate-pre-umi ERROR_RATE_PRE_UMI
- --error-rate-post-umi ERROR_RATE_POST_UMI
- --min-input-base-quality MIN_INPUT_BASE_QUALITY
- --min-consensus-base-quality MIN_CONSENSUS_BASE_QUALITY
- --min-reads MIN_READS
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)
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)
The Phred-scaled error rate for an error prior to the UMIs being integrated. (default: 45)
The Phred-scaled error rate for an error post the UMIs have been integrated. (default: 40)
Ignore bases in raw reads that have Q below this value. (default: 10)
Mask (make ‘N’) consensus bases with quality less than this threshold. (default: 2)
The minimum number of reads to produce a consensus base. (default: 2)
Common options:
- --logfile LOGFILE
- --tmp-dir TMP_DIR
- --with-petagene-dir WITH_PETAGENE_DIR
- --keep-tmp
- --license-file LICENSE_FILE
- --no-seccomp-override
- --version
Path to the log file. If not specified, messages will only be written to the standard error output. (default: None)
Full path to the directory where temporary files will be stored.
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.
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.