gatk.depthOFcoverage: gatk.depthOFcoverage

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

Description

Calculate the read depth of the position with single nucleotide variations

Usage

gatk.depthOFcoverage(vcf.dir, annot.dir, Robject.dir, ref.fa, unsafe,
  minBaseQuality = 1, minMappingQuality = 1, run.cmd = TRUE,
  mc.cores = 1)

Arguments

vcf.dir	Output of variant call step (directory of vcf files)
annot.dir	Output of annotation step (directory of .annovar files)
ref.fa	Reference fasta file path
unsafe	A parameter value for -U ALLOW_N_CIGAR_READS in GATK. This parameter must be TRUE in RNA-seq data.
minBaseQuality	Minimum base quality (default=1)
minMappingQuality	Minimum mapping quality (default=1)
run.cmd	Whether to execute the command line (default=TRUE)
mc.cores	The number of cores to dedicate. Must be at least one(default=1), and parallelization requires at least two cores.

Details

When creating a vSet, use read depth to determine whether a mutation exists. GATK DepthOfCoverage uses the interval bed file to calculate the depth of the position.

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