multiple.reads.pileup: multiple.reads.pileup

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

Description

A wrapper function to run samtools (mpileup)

Usage

multiple.reads.pileup(ref.fa, normal.bam, tumor.bam, sample.name, output.dir, mapQ=1, run.cmd=TRUE, mc.cores=1)

Arguments

ref.fa	Reference fasta file path
normal.bam	Path to normal sample recalibration bam files
tumor.bam	Path to tumor sample recalibration bam files as tumor-normal pair
sample.name	A character vector for the sample names
output.dir	Output directory
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.
mapQ	A parameter value for mapQ in varscan2. Skip alignments with mapQ smaller than mapQ value (default:1)

Details

Generate VCF, BCF or pileup for one or multiple BAM files. Alignment records are grouped by sample (SM) identifiers in @RG header lines. If sample identifiers are absent, each input file is regarded as one sample.

See Also

{http://www.htslib.org/doc/samtools.html

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