Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
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