VCF SNP Annotation

[ashkot]

Hi all, I am relatively new to this area and I wanted some with annotating VCF files. I converted a BAM file from 1KGenomes to VCF and I want to annotate that with dbSNP rsid.

Can someone please help me with the most simple way to annotate the VCF files?

Thanks in advance.

Ashwin

[Heisman]

Not entirely sure what you are asking but if you want the dbSNP rs numbers for a list of SNPs you can run them through a program called ANNOVAR (although that will only query up to dbSNP 132).

[ashkot]

Hi there, what i want is the following. After I have analyzed my data and have a VCF file ready, I want to run that file into some program that will assign the variants an rs id. I looked at ANNOVAR, is there another one that can also accomplish the same?

[Heisman]

You can look into using SeattleSeq: http://snp.gs.washington.edu/SeattleSeqAnnotation/

[krawitz]

www.gene-talk.de can do the annotation for you. all you have to do is uploading your vcf. it is a free annotation, filtering and interpretation tool for human sequence variants.