A Method to identify MultiSV from RDbin files for different samples defined in Configuration File

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Description

This is the main function to identify SVs. It works after the data has been prepared using Bin2MultiSV from bam files. Bin2MultiSV will prepare the data for MultiSV package and CallMultiSV will identify SVs.

Usage

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CallMultiSV(CfgFile, LgLim, SVSize, MtlSVOut)

Arguments

CfgFile

: A tab separated file with the following format (with no header)

Contrast SampleID PathtoRDbinFile

Treat Sample1 ~/Sample1.WindowRD-1000.count

Control Ref1 ~/Ref1.WindowRD-1000.count

Contrast SampleID PathtoRDbinFile

LgLim

: log2 limit, set 0.6 or higher

SVSize

: Minimum size of SV to identify, set 5000 or higher

MtlSVOut

: Output file

Details

Data Input from read depth (RD) bins

Value

CallMultiSV:

Author(s)

Khurram Maqbool

See Also

Bin2MultiSV

Examples

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## Not run: 
CallMultiSV(CfgFile, LgLim, SVSize, MtlSVOut)

## End(Not run)