Hi,

The software snpEFF could give you the effect of SNP/InDel to your candidate gene

Best!

Hi,

Try plink. It is very good at association analysis and QC steps. You can calculate association for dominant, additive and recessive inheritance models as well, just have a look at the manual for the commands http://pngu.mgh.harvard.edu/~purcell/plink/

I agree with Nesli, plink is good and fast. If you prefer graphic interface try Haploview (Mac, PC) for case-control or family-based association tests.https://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/downloads