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?
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..
You can use "SnpSift" (specifically "SnpSift concordance" command)
There is a tool that does it for you. Actually it can do a lot more than comparing vcf files.
Thanks! I'm using vcf-isec.
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