somaticsniper_workflow¶
Somatic sniper workflow to generate VCF from BAM/CRAM input files.

Quick Start¶
$ pbrun somaticsniper_workflow \
--ref Ref/Homo_sapiens_assembly38.fasta \
--in-tumor-bam tumor.bam \
--in-normal-bam normal.bam \
--out-prefix output
Compatible CPU Command¶
The commands below are the CPU 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.
bam-somaticsniper -q 1 -G -L -F vcf -f Ref/Homo_sapiens_assembly38.fasta tumor.bam normal.bam output.vcf
bcftools mpileup -A -B -d 2147483647 -Ou -f Ref/Homo_sapiens_assembly38.fasta tumor.bam | bcftools call -c | vcfutils.pl varFilter -Q 20 | awk 'NR > 55 {print}' > output.indel_pileup_Tum.pileup
perl snpfilter.pl --snp-file output.vcf --indel-file output.indel_pileup_Tum.pileup
perl prepare_for_readcount.pl --snp-file output.vcf.SNPfilter
bam-readcount -b 15 -f Ref/Homo_sapiens_assembly38.fasta -l output.vcf.SNPfilter.pos tumor.bam > output.readcounts.rc
perl fpfilter.pl -snp-file output.vcf.SNPfilter -readcount-file output.readcounts.rc
perl highconfidence.pl -snp-file output.vcf.SNPfilter.fp_pass.vcf
somaticsniper_workflow Reference¶
Run the somaticsniper 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 the BAM file for tumor reads. (default: None)
Option is required.
- --in-normal-bam IN_NORMAL_BAM
Path of the BAM file for normal reads. (default: None)
Option is required.
- --out-prefix OUT_PREFIX
Prefix filename for output data. (default: None)
Option is required.
Tool Options:¶
- --num-threads NUM_THREADS
Number of threads for worker. (default: 1)
- --min-mapq MIN_MAPQ
Filter reads with mapping quality less than this value. (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.