vcf-compare and making Venn diagram
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2.5 years ago
arshad1292 ▴ 90


I want to compare two vcf files using vcf tools, and draw the Venn diagrams to visualize the comparison.

I ran the following command.

vcf-compare file1_sniffles_filtered.vcf file2_Chr.vcf --ignore-indels -r -p

Here is the output:

VN 'Venn-Diagram Numbers'. Use grep ^VN | cut -f 2- to extract this part.

VN The columns are:

VN 1 .. number of sites unique to this particular combination of files

VN 2- .. combination of files and space-separated number, a fraction of sites in the file

VN 1 file2_Chr.vcf (0.0%) file1_sniffles_filtered.vcf (0.0%) VN 2433 file1_sniffles_filtered.vcf (100.0%) VN 708961 file2_Chr.vcf (100.0%)

SN Summary Numbers. Use grep ^SN | cut -f 2- to extract this part.

SN Number of REF matches: 0 SN Number of ALT matches: 0 SN Number of REF mismatches: 1 SN Number of ALT mismatches: 0 SN Number of samples in GT comparison: 0

Number of sites lost due to grouping (e.g. duplicate sites): lost, %lost, read, reported, file

SN Number of lost sites: 268 9.9% 2702 2434 file1_sniffles_filtered.vcf SN Number of lost sites: 449 0.1% 709411 708962 file2_Chr.vcf

Question 1: Is that the right output that I am supposed to get? Question 2: How can I create Venn diagram using these results?

I tried looking up online and found some 5-6 years old thread but that method doesn't work anymore, I guess.

Please help this newbie. Many thanks in advance.

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