MuSE.call: MuSE.call

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

Description

A wrapper function to run MuSE (call)

Usage

MuSE.call(tumor.bam, normal.bam, output.dir, sample.name, ref.fa, run.cmd=TRUE, mc.cores=1)

Arguments

tumor.bam	path to tumor sample recalibration bam files as tumor-normal pair
normal.bam	path to normal sample recalibration bam files
output.dir	Output directory
sample.name	A character vector for the sample names
ref.fa	Reference fasta file
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 first step of MuSE, MuSE.call takes as input indexed reference fasta file and BAM files. The BAM files require aligning all the sequence reads against the reference genome using the Burrows-Wheeler alignment tool BWA-mem algorithm. In addition, the BAM files need to be processed by following the GATK-MarkDuplicates, realigning the paired tumor-normal BAMs jointly and recalibrating base quality scores.

Value

MuSE.call output txt file.

References

MuSE: accounting for tumor heterogeneity using a sample-specific error model improves sensitivity and specificity in mutation calling from sequencing data

See Also

http://bioinformatics.mdanderson.org/main/MuSE

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