read.pileup.gz: read.pileup.gz

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

read.pileup.gz(ref.fa, fns.bam, sample.name, output.dir, mapQ=1, run.cmd=TRUE, mc.cores=1)

Arguments

ref.fa	Reference fasta file path
sample.name	A character vector for the sample names
mapQ	Mapping quality (default=1)
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.
normal.bam	BAM files of normal sample
tumor.bam	BAM files of tumor sample

Details

Generates VCF, BCF or pileup for one or multiple BAM files. Alignment records are grouped by sample (SM) identifiers in @RG header lines. If the 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.