MuSE.sump: MuSE.sump

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

Description

A wrapper function to run MuSE (sump)

Usage

MuSE.sump(MuSE.txt, output.dir, ref.dbSNP, ref.gold_indels, data.type="E", run.cmd=TRUE, mc.cores=1)

Arguments

MuSE.txt	Path to MuSE.call output text file
output.dir	Output directory
MuSE.data.type	E is used for WXS data and G can be used for WGS data
ref.dbSNP	Known SNP sites reference
ref.gold_indels	Known Indel sites reference
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 second step, MuSE sump, takes as input the output file from MuSE.call and dbSNP variant call format file. MuSE provide two options for building the sample-specific error model. One is applicable to WES data (option ‘-E’), and the other to WGS data (option -G).

Value

vcf files included variant call information

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.