Lior Pachter on read alignment in general is a good start[1].   
This package seems to modify the human reference genome based on the known mutations a person has, making it easier to map an exon back to a genomic position.<p>[1] <a href="https:&#x2F;&#x2F;liorpachter.wordpress.com&#x2F;2015&#x2F;11&#x2F;01&#x2F;what-is-a-read-mapping&#x2F;" rel="nofollow">https:&#x2F;&#x2F;liorpachter.wordpress.com&#x2F;2015&#x2F;11&#x2F;01&#x2F;what-is-a-read-...</a>