I am working on SNP analysis. Sequencing was performed by Molecular Inversion Probe (MIP)-based re-sequencing. I have BAM files right now, and I am trying to eliminate reads with more than five variations from the reference per read, with the exception of multi-basepair insertions and deletions.

I am student, beginner, and have not found a way to perform it. All ideas are welcomed.

Is there a tool to find a number of variations from the reference per read?