Compare NGS data with dbSNP

[lyz1030]

Hi,

Now, I have a vcf file containing all the SNPs that I have used Samtools to find. How can I relate it to dbSNP and find out which are novel SNPs and the rs number of existed ones? What tools can I use and what datasets do I　need to download?

[ulz_peter]

Hi Lyz,

Check out Annovar.

http://www.openbioinformatics.org/annovar/

Go to filter-based annotations at point 3 there are detailed instructions how to annotate or filter SNPs from dbSNP!

One short notice: Be careful when dealing with dbSNP data. Do NOT discard mutations when finding them in dbSNP, especially using the later releases (version > 130)