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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_mutation_cell_fraction
    minimum fraction of cells which are presumed to have a mutation, used to handle non-clonality and contamination


Best Answer


  • ParthavJailwalaParthavJailwala MarylandMember

    Thanks Geraldine!

  • vivekdas_1987vivekdas_1987 MilanMember

    I would like to ask in this thread is there anyway to use some kind of paramters that can speicify if my tumor is 70% pure which means 30% have normal cell contamination in my tumor sample. I was expecting the fraction_contamination paramter or minimum_mutation_cell_fraction. I would like to know if any new parameter is introduced or not?

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Not in the current version, no. The fraction_contamination parameter refers to contamination between samples. The mutation cell fraction (or purity) cannot currently be specified or taken into account in a really effective way. Future developments may address this.

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