Hi Vishal,

SNPs with excessively high read depth are usually caused by alignment artifacts or structural variations and should not be trusted. I use to set the Maximum Read Depth to the 175% of the average coverage, but I need high confidence SNPs.

You can even increase that value to 3 or 5 x that of the mean coverage, but remember that setting the value too high will result in too many false positives, otherwise SNPs will not be reported for those regions with coverage > '-D'.

I hope this will help you,

best.