I want to check how often the sequence TGAT is inserted or deleted in different strains of mouse. I downloaded VCF files containing SNPs and Indels for each strain from the Mouse Genomes Project. I can grep the indels file for my sequence and count how many times it appears in the REF/ALT columns. However, a single nucleotide change can also change the frequency. I was going to write a script to get the SNP coordinates and check if they were inside a TGAT sequence from the reference genome, but wanted to check if anyone knows or a tool which may answer my question, or even a better way to measure what I want?