somaticsniper_workflow

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

../../_images/sniper.png

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.