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.
$ 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
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
Identify single nucleotide positions that are different between tumor and normal BAM files.
Input/Output file options
- --ref REF
- --in-tumor-bam IN_TUMOR_BAM
- --in-normal-bam IN_NORMAL_BAM
- --out-file OUT_FILE
Path to the reference file. (default: None)
Option is required.
Path of BAM/CRAM file for tumor reads. (default: None)
Option is required.
Path of BAM/CRAM file for normal reads. (default: None)
Option is required.
Path of output file. (default: None)
Option is required.
Options specific to this tool
- --num-threads NUM_THREADS
- --min-mapq MIN_MAPQ
- --out-format OUT_FORMAT
- --correct
- --no-gain
- --no-loh
Number of threads for worker. (default: 1)
Filtering reads with mapping quality less than this value. (default: 0)
Type of output format. Possible values are {classic, vcf}. (default: classic)
Fix baseline bugs. If this option is not passed, the same output will be generated as baseline. (default: None)
Do not report Gain of Reference variants as determined by genotypes. (default: None)
Do not report LOH variants as determined by genotypes.
(default: None)
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.