What kind of sequencing data and what kind of organism are you considering? Also, how many mutants do you have?

Anyway, a tool you can try is Ensembl Variant Effect Predictor. The first step is to identify variants (use GATK maybe) , filtering out sequencing errors.

The FASTA package of alignment software provides programs for aligning a DNA query with a protein library (or sequence): fastx36 and fasty36, as well as compare a protein sequence to a DNA library (tfastx36, tfasty36). You probably want the tfasty36 program if you have a lot of DNA sequences (tfasty36 uses a more sophisticated frameshift algorithm than tfastx36, but it is also slower). The programs have some compact output options that would make it easy to sift through alignments for frameshifts.

http://faculty.virginia.edu/wrpearson/fasta/CURRENT/fasta36.tar.gz or

http://github.com/wrpearson/fasta36

Hello apology for late reply,

I often use translatorX for sequence alignment where you can get aligned protein sequence as well as DNA sequence alignment.

Thanks.