I am putting this question because I did not find any useful information from internet because of limited access. My question is related to control (or normal) data that we use for somatic mutation detection (with the help of mutect or SomaticSnipper etc) with tumor data. Here are the questions:
- What information (type of files and information within files) we can actually get from control data.
- Does control data tell us about germline mutations of the patient (may be due to this reason we use same patient tumor-only and normal data for somatic mutation detection.
- If my assumption in Q2 is right than is there any consensus list of mutations contained in normal data for a specific cancer type (I mean to say if there is any data which contains all germline mutations that can be helpful to specific cancer)
- From where I can get all information about controlled (normal) data. (I think it is locked everywhere)
- In case of Blood cancer (Multiple Myeloma), is it true that we can't have normal or controlled data. If yes than how can I find somatic mutations.
In case of any wrong assumption or misconception, please correct me.