somaticsniper: somaticsniper

In omicsCore/SEQprocess: SEQprocess : a modularized and customizable pipeline framework for NGS processing in R package.

Description

A wrapper function to run SomaticSniper

Usage

somaticsniper(ref.fa, tumor.bam, normal.bam, output.dir, sample.name, mapQual=1, LOH=TRUE, Genotype=TRUE, somaticQual=15, somaticMutation=0.01, Theta=0.85, Hap.number=2, Hap.diff=0.001, out.format="vcf", run.cmd=TRUE, mc.cores=1)

Arguments

tumor.bam	Tumor sample bam files
normal.bam	Normal sample bam files
output.dir	Output directory
sample.name	A character vector for the sample names
ref.fa	Reference fasta file
mapQual	A parameter value for -q in SomaticSniper Filtering reads with mapping quality less than INT (default:1)
LOH	A parameter value for -L in SomaticSniper. Do not report LOH variants as determined by genotypes (logical)
Genotype	A parameter value for -G in SomaticSniper. Do not report Gain of Referene variants as determined by genotypes (logical)
somaticQual	A parameter value for -Q in SomaticSniper. Filtering somatic SNV output with somatic quality less than INT (default:15)
somaticMutation	A parameter value for -s in SomaticSniper. Prior probability of a somatic mutation (default:0.01)
Theta	A parameter value for -T in SomaticSniper. Theta in maq consensus calling model (default:0.85)
Hap.number	A parameter value for -N in SomaticSniper. Number of haplotypes in the sample (default:2)
Hap.diff	A parameter value for -r in SomaticSniper. Prior of a difference between two haplotypes (default:0.001)
out.format	A parameter value for -F in SomaticSniper. Select output format (vcf or classic) (default:vcf)
run.cmd	Whether to execute the command line (default=TRUE)
mc.cores	The number of cores to use. Must be at least one(default=1), and parallelization requires at least two cores.

Details

The purpose of this program is to identify single nucleotide positions that are different between tumor and normal (or in theory, any two bam files). It takes a tumor bam and a normal bam and compares the two to determine the differences.

Value

VCF files

References

SomaticSniper: identification of somatic point mutations in whole genome sequencing data.

See Also

http://gmt.genome.wustl.edu/packages/somatic-sniper/

omicsCore/SEQprocess documentation built on May 7, 2020, 4:18 a.m.