<p>Hi</p>

<p>Can anyone help in SNP analysis. Which online tool should I use to get the data for SNP.</p>

Owhkee, so you did something like create a bowtie database (or bwa or whatever mapper you used), then aligned your reads or query against your indexed reference. Then you piped that to a Sam or Bam file right?

Well now you can do SNP calling, there are a lot of tools, i use Freebayes but I have also used Samtools Mpileup and BCFtools to get SNPs but for me freebayes works the best.

If you have more specific questions just aks, but i would first just read a little about SNP calling tools so you know for sure that you have the right tool for your project. And read the manuals to understand what the tools do. For freebayes you can look at [this tutorial](http://clavius.bc.edu/~erik/CSHL-advanced-sequencing/freebayes-tutorial.html).