strelka_workflow
Strelka workflow to generate VCF files from BAM/CRAM input files.
$ pbrun strelka_workflow \
--ref Ref/Homo_sapiens_assembly38.fasta \
--in-tumor-bam tumor.bam \
--in-normal-bam normal.bam \
--out-prefix output
The commands below are the GATK4 counterpart of the Parabricks command above. The output from these commands will be identical to the output from the above command. See the Output Comparison page for comparing the results.
mkdir -p manta_work
python $MANTA_DIR/bin/configManta.py \
--referenceFasta Ref/Homo_sapiens_assembly38.fasta \
--normalBam normal.bam \
--tumorBam tumor.bam \
--runDir manta_work
cd manta_work
python ./runWorkflow.py -m local -j ${MAX_NUM_PROCESSORS}
cd ..
mkdir -p strelka_work
python $STRELKA_PATH/configureStrelkaSomaticWorkflow.py \
--referenceFasta Ref/Homo_sapiens_assembly38.fasta \
--normalBam normal.bam --tumorBam tumor.bam \
--indelCandidates ${WORK_PATH}/manta_work/results/variants/candidateSmallIndels.vcf.gz \
--runDir strelka_work
cd strelka_work
python ./runWorkflow.py -m local -j ${MAX_NUM_PROCESSORS}
cd ..
Run the strelka variant caller workflow.
Input/Output file options
- --ref REF
- --in-tumor-bam IN_TUMOR_BAM
- --in-normal-bam IN_NORMAL_BAM
- --bed BED
- --out-prefix OUT_PREFIX
Path to the reference file. (default: None)
Option is required.
Path of the BAM/CRAM file for tumor reads. (default: None)
Option is required.
Path of the BAM/CRAM file for normal reads. (default: None)
Option is required.
Optional bgzip-compressed/tabix-indexed BED file containing the set of regions to call. (default: None)
Prefix filename for output data. (default: None)
Option is required.
Tool Options:
- --num-threads NUM_THREADS
Number of threads for worker. (default: 1)
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.