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Somatic mutation not being called as somatic
I am using Mutect to call somatic variants in my sample from a known EGFR mutant patient. I find that the EGFR mutation is rejected by mutect. The extended output gave the reason being "alt_allele_in_normal". I see 5 reads out of total 153 reads in the normal supporting the variant allele (which could also be due to tumor contamination in the normal). I want this mutation to be called as somatic. What parameters do I change during the mutect run ? I have attached the extended output for you to have a look.
Also is there place where I can find all the options which can be used in mutect run and the default values. Further I would like to know the default values for read count, allele frequencies cut offs in mutect used for calling variants in tumor and normal. The help menu of mutect (with -h option) does not give these and also the --enable-extended-output option doesn't appear in the help menu (found it in one of the threads so could use it). Is there a location where there is better documentation of all the parameters of mutect ?