1)Filter out low-quality variants(<100):
perl Filter_Quality.pl demo.vcf > filter1.txt 100
#Expected output:filter1.txt
2)Select variants with appropriate depth(5%~95%):
perl Filter_Depth.pl filter1.txt > filter2.txt 3 0.05 0.95
#Expected output:filter2.txt
3)Filter out SNPs that show none reference reads:
perl Filter_SNP.pl filter2.txt > filter3.txt 3 1 2 3
#Expected output:filter3.txt
4)Calculate p-value 
perl Ridit.pl filter3.txt > pvalue.txt 1 2 3 
#Expected output:pvalue.txt
5)Denoise strategy 
perl denoise.pl pvalue.txt > ratio.txt 4 10 12
#Expected output:ratio.txt
6)Generate P-value plot
Rscript pos-pvalue.R
#Expected output:pvalue.png
7)Generate ratio plot
Rscript pos-ratio.R
#Expected output:ratio.png
8)Identify peak interval 
 perl p-max.pl ratio.txt 6
 #Expected output:Standard screen output