I targetted a protein-coding exon with Cas9, amplified a ~ 150bp product in the region and sequenced with Illumina MiSeq. I now have > 1000X coverage of the region, mapped to my reference genome. Many of these reads have indels, thus potentially inducing a frameshift (if not a multiple of 3).

Is there any tool available to predict premature stop codons in my reads (or even non-sense mediated decay)?

I should add I do not want to create an assembly/consensus of my reads. That is because there is mosaicism in the mutations induced by Cas9 (eg. half of my reads have a 1bp deletion, the other half have a 9bp insertion). In the simplest form, I would want a tool that scans for stop codons each of my mutated read, and in the correct frame (i.e. the frame used by the cell to translate that specific mRNA).