Annotating variants using latest version fof the genome

Question

[prasundutta87]

Hi,

I have SNP data from an array which has coordinate information from an older version of the genome (in VCF form). I want to annotate it using GTF/GFF file of the current version of the genome using SnpEff or ANNOVAR or VEP. Do I need to take care of the VCF coordinates somehow (like liftover) so that the variant annotation program can annotate the variants correctly?

Or, the variant annotation program will only annotate the variants with matching coordinates and incorrectly annotate the rest whose coordinates don't match?

I am assuimg its the second, but want other people's opinion on this.

Regards, Prasun

Answer 1

[GenoMax]

You could use crossmap (LINK) to first convert the co-ordinates over to the version of the genome you want to use and then annotate.

[prasundutta87]

Thanks all..I believe that I have got an answer to my query and I am thinking in the right direction!

Answer 2

[brunobsouzaa]

Just to check if I understood, you have SNP data with hg19 coordinates and you want to annotate with hg38 coordinates? Don't do this, use the same genome version to annotate your files.

[prasundutta87]

As an hypothetical example, yes, that's exactly what I am asking and I am hoping that the coordinates will all screw up giving all sort of wrong annotations..

[brunobsouzaa]

If you use different genome versions yes, it will give you wrong annotations!