somaticsniper

Accelerated Somatic Sniper, which supports tumor-normal variant calling. Parabricks features Somatic Sniper as a standalone tool, or you can use the Somatic Sniper workflow to generate a VCF file from BAM/CRAM.

Quick Start

$ pbrun somaticsniper \
    --ref Ref/Homo_sapiens_assembly38.fasta \
    --min-mapq 1 \
    --no-gain \
    --no-loh \
    --in-tumor-bam tumor.bam \
    --in-normal-bam normal.bam \
    --out-file output.vcf

Compatible CPU Command

The command below is the 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.

bam-somaticsniper -q 1 -G -L -F vcf -f  Ref/Homo_sapiens_assembly38.fasta  tumor.bam normal.bam output.vcf

somaticsniper Reference

Identify single nucleotide positions that are different between tumor andnormal BAM files.

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.

--out-file OUT_FILE

Path of output file. (default: None)

Option is required.

Options specific to this tool

--num-threads NUM_THREADS

Number of threads for worker. (default: 1)

--min-mapq MIN_MAPQ

Filtering reads with mapping quality less than this value. (default: 0)

--out-format OUT_FORMAT

Type of output format. Possible values are {classic, vcf}. (default: classic)

--correct

Fix baseline bugs. If this option is not passed, the same output will be generated as baseline. (default: None)

--no-gain

Do not report Gain of Reference variants as determined by genotypes. (default: None)

--no-loh

Do not report LOH variants as determined by genotypes.

(default: None)

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.