How to compare 2 VCF files

Question

[Parimala Devi]

Hey,

I have 2 vcf files. I want to compare the two, and save the SNPs that are common to both in a separate file, also save SNPs that are present only in 2nd file in another file.

Which tool do I use for this?

Thank you,
Parimala

[aaarsh88]

i have file with three coloumns first coloumn containing the frequency of scaffolds(i.e. in 2nd coloumn) . Therefore i want to filter the file with coloumn having high count number in new file..

Thanx

Answer 1

[Pablo]

You can use "SnpSift" (specifically "SnpSift concordance" command)

Answer 2

[Ashutosh Pandey]

There is a tool that does it for you. Actually it can do a lot more than comparing vcf files.

VCFtools

[Parimala Devi]

Thanks! I'm using vcf-isec.

[Ashutosh Pandey]

Great.