I'm using the Varscan tool to call SNPs and INDELs. There are some TRUE variants that are not called by this variant caller. I can clearly see them with IGV. For example there are 34 reads at a loci with all being mutant reads (100%), and still not called as a variant. I used a minimum read depth of 3 and a base quality score of 24 to call these variants. The reads seems to be in good quality. This variant is still not called even if I reduce the base quality score. Can some one explain me the reason, why this variant might not have been called.