SNP annotation in sequence

Question

[morgen]

Hi,

I am new to the field of bioinformatics and just starting to gather information about the available resources. I am sequencing a candidate gene in some DNA samples in a case-control design to identify rare as well as common disease-associated variants, and I want to annotate all SNPs on the RefSeq gene and then compare sample sequences. Any general suggestion on how to approach sequence data? Thanks for your help

Best regards,
Morgen

Answer 1

[iraun]

If you want to annotate a set of SNPs of a vcf file, I would suggest you to use SnpEff. It is widely used for annotate variants and it supports more than 20.000 genomes. Also SnpEff has a very user friendly manual, in which you can learn easily how to costumize without troubles. Besides the annotation, SnpEff also is able to do a prediction of the effect of the given variant (such as amino acid changes).

Of course there are another tools which could do the annotation, I've just mention my favorite one.

Answer 2

[kautilya]

For annotation of SNPs you can also use SeattleSeq Variation Annotation. It simple to use - you upload your snps in a .vcf or any of the other supported formats, select the annotations you want and get the annotated output.

As for the comparison I guess you want o compare the variants found in different sample for this you could call the variations using a tool which supports multi-sample calling like the GATK UnifiedGenotyper and use the PLINK suite for comparison purposes.