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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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Plotting the comparison of multiple input VCF files after merging shows only coincidental cases #151

Closed dKlee99 closed 3 years ago

dKlee99 commented 3 years ago

Hi, thanks for providing this amazing tool! I 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 0 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,

image

1631639473793

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

Nazeeefa commented 3 years ago

@dKlee99 In response to your question in #101; I wrote following to see overlap between three dataset i.e:

venn.diagram(list
             (File1=which(t[,1]==1), File2=which(t[,2]==1), File3=which(t[,3]==1)) , 
             fill = c("colour1", "colour2", "colour3") , 
             alpha = c(0.5, 0.5, 0.5), 
             cex = 2, lty =2, ext.text=TRUE, 
             filename = "output.jpeg")
dKlee99 commented 3 years ago

@dKlee99 In response to your question in #101; I wrote following to see overlap between three dataset i.e:

venn.diagram(list
             (File1=which(t[,1]==1), File2=which(t[,2]==1), File3=which(t[,3]==1)) , 
             fill = c("colour1", "colour2", "colour3") , 
             alpha = c(0.5, 0.5, 0.5), 
             cex = 2, lty =2, ext.text=TRUE, 
             filename = "output.jpeg")

It worked! Thank you so much!!