SURVIVOR merge function usage

Question

[dlekrud456]

Hello,

I have issues with SURVIVOR merge function that only shows coincidental cases when I draw VenDiagram. Can anyone please help me with this issue?

used survivor merge and genComp function to compare two vcfs but it only shows coincidental cases. The below is my code.

In bash,

SURIVOR merge sample_files 1000 2 1 1 0 30 sample_merged.vcf
genComp sample_merged.vcf sample_merged.mat.txt
perl -ne 'print "$1\n" if /SUPP_VEC=([^,;]+)/' sample_merged.vcf | sed -e 's/\(.\)/\1 /g' > sample_merged_overlapp.txt

In R,

t=read.table("sample_merged_overlapp.txt",header=F)

library(VennDiagram)

venn.diagram(list(N15=which(t[,1]==1), T15=which(t[,2]==1)), fill = c("gray", "orange") , alpha = c(0.5, 0.5), cex = 2, lty =2, filename = "my_sample")

And the result shows following,

I'm new to programming and not sure how to solve this issue, your help is very much appreciated!