Tool for SNP calling and annotaion

[mathew]

I have paired end seq data and would like to compare three samples for differential SNPs. I guess I need to first call SNPs and then annotate it with known genes. IS there any tool (GUI based???) which need least level of programming skills.
So basically the tool should first be calling SNPs and then perform statistical analysis to call significant or true SNPs and same or another tool may provide annotation. Any pointers will be great

Thanks

[adamyao]

For annotation tool with GUI, there are some. One of them is VarioWatch (http://genepipe.ncgm.sinica.edu.tw/variowatch). It provides online real time annotation on millions of variants in just a few minutes.

[Morgane_AUS]

VarioWatch is for human only, is there a similar program for bacterial genomes ?