strelka_workflow

Strelka workflow to generate VCF files from BAM/CRAM input files.

../../_images/strelka.png

Quick Start

$ pbrun strelka_workflow \
    --ref Ref/Homo_sapiens_assembly38.fasta \
    --in-tumor-bam tumor.bam \
    --in-normal-bam normal.bam \
    --out-prefix output

Compatible GATK4 Command

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 ..

strelka_workflow Reference

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)

--keep-tmp

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.

--no-seccomp-override

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

--version

View compatible software versions.