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.