Call variants with high sensitivity, predicting variants below the average base-call quality (Original Lofreq Project). The call part is accelerated.
pbrun lofreq_call is the Parabricks equivalent of the original lofreq call.
pbrun lofreq is the Parabricks equivalent of the original lofreq somatic.
$ pbrun lofreq_call \
--ref Homo_sapiens_assembly38.fasta \
--in-bam the_input.bam \
--out out.vcf.gz
Note that the value for --out is the name of the output file, whereas in
the Parabricks lofreq tool --output-dir is the name of an output directory.
The command below is the original CPU counterpart of the Parabricks command above. The output from this command will be identical to the output from the above command. See the Output Comparison page for comparing the results.
lofreq call -f Homo_sapiens_assembly38.fasta \
-o out.vcf.gz \
the_input.bam
Call variants from BAM file
Input/Output file options
- --ref REF
- --in-bam IN_BAM
- --ign-vcf IGN_VCF [IGN_VCF ...]
- --out OUT
Indexed reference fasta file. (default: None)
Option is required.
Path of the BAM/CRAM file. This option is required. (default: None)
Option is required.
Ignore variants in this vcf file for source quality computation. Multiple files can be given separated by space (default: None)
Vcf output file. (default: None)
Option is required.
Tool Options:
- --num-threads NUM_THREADS
- --min-bq MIN_BQ
- --min-alt-bq MIN_ALT_BQ
- --min-jq MIN_JQ
- --min-alt-jq MIN_ALT_JQ
- --no-baq
- --no-idaq
- --del-baq
- --no-ext-baq
- --min-mq MIN_MQ
- --max-mq MAX_MQ
- --no-mq
- --src-qual
- --def-nm-q DEF_NM_Q
- --sig SIG
- --bonf BONF
- --min-cov MIN_COV
- --illumina-1-3
- --use-orphan
- --no-default-filter
- --force-overwrite
Number of threads per GPU. (default: 1)
Skip any base with baseQ smaller than INT. (default: 6)
Skip alternate bases with baseQ smaller than INT. (default: 6)
Skip any base with joinedQ smaller than INT. (default: 0)
Skip alternate bases with joinedQ smaller than INT. (default: 0)
Disable use of base-alignment quality (BAQ) (default: None)
Don circumstances other than debugging) (default: None)
Delete pre-existing BAQ values, i.e. compute even if already present in BAM (default: None)
Use extended BAQ (both computed on the fly if not already present in lb tag) (default: None)
Skip reads with mapping quality smaller than INT. (default: 0)
Cap mapping quality at INT. (default: 255)
Don (default: None)
Enable computation of source quality (default: None)
If >= 0, then replace non-match base qualities with this default value. (default: -1)
P-Value cutoff / significance level. (default: 0.01)
Bonferroni factor. INT (default: 1)
Test only positions having at least this coverage. (default: 1)
Assume the quality is Illumina-1.3-1.7 encoded (default: None)
Count anomalous read pairs (i.e. where mate is not aligned properly) (default: None)
Don calling variants (default: None)
Overwrite any existing output (default: None)
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.
GPU options:
- --num-gpus NUM_GPUS
- --gpu-devices GPU_DEVICES
Number of GPUs to use for a run. GPUs 0..(NUM_GPUS-1) will be used.
GPU devices to use for a run. By default, all GPU devices will be used.
To use specific GPU devices, enter a comma-separated list of GPU device
numbers. Possible device numbers can be found by examining the output of
the nvidia-smi command. For example, using --gpu-devices 0,1
would only use the first two GPUs.