I have a question, it would be appreciable if someone can give some ideas or suggestions to me regarding my question. I am analyzing exome data for normal samples , its corresponding tumor and its IPS derived from the tumor. I want to know even before calling the variants is there are way I can do a global check on my samples based on the reads to understand whether the IPS resembles the wild type or the tumor samples more or not. Can I make a calling on the reads between the tumor vs wild type and the IPS, based on any parameter that can help me map or enable me to mirror globally where the IPS resemble the wild type more or the tumor exomes. I am not sure how to achieve this on read level. But still I would like to give it a try, if we use the exome bed files provided by the company to see which coordinates lie on the exonic region for each tumor, wild-type and IPS based on the reads and then compare those coordinates to see the overlap of the coordinates having the reads between tumor vs wild type and tumor vs IPS to understand whether the tumor is more close to the wild type or IPS. Is this feasible? If so then I would like to have suggestions about it and how to achieve this? Is there script publicly available to do this?