Request for more information on Mutect parameters
I am looking for more information on the description / use of these muTect parameters:
a) Related to a family pedigree:
-pedigree Pedigree files for samples
-pedString, Pedigree string for samples
-pedValidationType How strict should we be in validating the pedigree information?
If the goal is to find somatic mutations in tumor-normal pairs from a trio (Father, Mother, affected child), how is the pedigree information factored in , in the somatic calls ?
b) I understand that there is no parameter to factor in the tumor purity, as the variant calling algorithm models the allele frequencies from the data. However, I am wondering if this parameter can be used indirectly to specify the tumor purity. For eg, if the tumor is 85% pure, can this parameter be set to 0.85 ?
minimum fraction of cells which are presumed to have a mutation, used to handle non-clonality and contamination