Help with SNP analysis

[JdevSEQnoob]

Hi, I'm new to the sequencing analysis. in the project that im working on, I have a list of SNP positions by chromosome, region and the reference allele call. However I have been retasked with annotating these SNPs back to a reference genome. Can anyone help direct me or help me get my path started? Thanks!

-JDev.

[HESmith]

The simplest approach is to convert the data you have to VCF format, then use one of the annotation tools (e.g., ANNOVAR or snpEff). Be sure that you're using the same version of the reference used for the original SNP calls, or the results will be meaningless.

[JdevSEQnoob]

ok, so I've got my SNPs annotated. now what is the best way to visualize this data. which program helps put all these points along a reference genome to look at?

[GenoMax]

You should be able to use IGV or UCSC browser to visualize the tracks.