Hi everyone:

I have successfully found some snps from whole exome data, mainly through samtools.

But I want to make a shorter list containing the more convincing snps. I guess read depth is important, what else should I consider?

I would like to hear your experience and suggestions. How did you select snps practically?

Besides, I used the default parameter to call snps, in which BAQ is enabled. In may case the coverage is around 25X. Should I use -E or -S instead to find more snps? How you usually use samtools to find snps?

Thanks.