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How to run ExCNVSS

1. Download the ExCNVSS source and sample data and java file of download page.


2. Unzip ExCNVSS source to some folder.

....
....- ExCNVSS.m : Main function
....- CNV_SSm22.m : Output CNV Result
....- load_data.m : Load Data
....- coverageReconstruct_By_segment_region.m : segmentation and normal distribution
....- cdfcalc22.m : plot the sample CDF staircase.
....- gConv.m : Gaussian kernel
....- diff2.m : Laplacian
....- LoGm22.m : Laplacian of Gaussian
....- RLEcode.m : Run Length Encoding
....- dtCNVm2.m : Detect CNV regions


3. Unzip the sample data.
....- control.bam, test.bam : bam file
....- control.coverage, test.coverage : coverage file
....- target_chr1.bed : target file(java input file)
....- target region.xlsx : target file(ExCNVSS input file)


4. Unzip java file.
....- coverage_zero_insert.class : Correct coverage data
....- ratio.class : Calculate ratio data(test/control)
....- vcf_args.class : Ouput format conversion to VCF


5. Preparing Input File
....ExCNVSS requires two major inputs. One is the read alignment results of test and control data, and the other is the
....target region information.

....5-1. Compute the depth at each position and generate Input Coverage Data
....- File : control.bam, test.bam, target_chr1.bed file
....- tool : Samtools
....- command : ex) ./samtools depth -b target_chr1.bed control.bam or test.bam &> control.coverage or test.coverage

....5-2. Correct Input Coverage Data
....- Fill the empty areas
....- File : control.coverage, test.coverage, target_chr1.bed, coverage_zero_insert.class
....- tool : java
.......

....5-3.Calculate Ratio Data
....- ratio(test/control)
....- File : cotrol_zero_insert.coverage, test_zero_insert.coverage, ratio.class
....- tool : java
.......

6. Running ExCNVSS<

....6-1. Run a MATLAB.
.......

....- ExCNVSS Directory
.......

....- Input File Format
.......
....- Select a folder that have source files.
.......

....- Input the run command.
.......

....- default option.
.......



7. Getting CNV Results

....7-1. Default Output Format
......
.......- Chr: Number of Chromosome
.......- Start: Start position of CNV
.......- Stop: Stop position of CNV
.......- Length: Length of CNV
.......- Type: 'Gain' or 'Loss'

....7-2. VCF Output Format
....- File : Referenc file, output file(6-1 result), vcf_args.class
....- tool : java
.......

....- Result File
......


Database Laboratory, Department of Computer Engineering, Hallym University, 1 Hallymdaehak-gil, Chuncheon, Gangwon-do 200-702, Korea