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/ \ --referenceFasta Ref/Homo_sapiens_assembly38.fasta \ --normalBam normal.bam \ --tumorBam tumor.bam \ --runDir manta_work cd manta_work python ./ -m local -j ${MAX_NUM_PROCESSORS} cd .. mkdir -p strelka_work python $STRELKA_PATH/ \ --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 ./ -m local -j ${MAX_NUM_PROCESSORS} cd ..

Run the strelka variant caller workflow.

Input/Output file options

--ref REF

Path to the reference file. (default: None)

Option is required.

--in-tumor-bam IN_TUMOR_BAM

Path of BAM/CRAM file for tumor reads. (default: None)

Option is required.

--in-normal-bam IN_NORMAL_BAM

Path of BAM/CRAM file for normal reads. (default: None)

Option is required.

--bed BED

Optional bgzip-compressed/tabix-indexed BED file containing the set of regions to call. (default: None)

--out-prefix OUT_PREFIX

Prefix filename for output data. (default: None)

Option is required.

Options specific to this tool

--num-threads NUM_THREADS

Number of threads for worker. (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)


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.


Do not override seccomp options for docker (default: None).


View compatible software versions.

© Copyright 2022, Nvidia. Last updated on Jun 28, 2023.