fraction_contamination and unrelated status
I recently used ASCAT to calculate percent contamination in a tumor specimen. I used array data to do this. I was also planning on checking this with contEst if I can get my SNP array calls into VCF format (Illumina HumanCoreExome array). That last big aside, I was wondering whether the --fraction_contamination input for MuTect was the appropriate place to input my percent contamination from ASCAT. I am confused by the documentation that states this input is for an "estimate of fraction (0-1) of physical contamination with other unrelated samples". The contamination I have is not from an unrelated sample it is basically the "normal" tissue contaminating the "tumor" tissue.
Is --fraction_contamination the appropriate place to input this data or is there another way to better incorporate this information in MuTect calling?
Thank you very much for your consideration.