Can anyone help me with interpreting VCF file file from Mutect2 variant calling.. I have followed the methods described for calling variants. The samples I am using are Tumor-Normal matching samples.
The resulting VCF file looks different from regular VCF file. I couldn't find any information regarding for interpreting the VCf file from MuTect2 caller.
Here is an example variant from the VCF file called using MuTect2
chrY 10036237 . A C . alt_allele_in_normal ECNT=1;HCNT=11;MAX_ED=.;MIN_ED=.;NLOD=8.64;TLOD=7.11 GT:AD:AF:ALT_F1R2:ALT_F2R1:FOXOG:QSS:REF_F1R2:REF_F2R1 0/0:86,8:0.091:7:1:0.125:2491,167:60:26
Where in all of the variants reported from my samples I have only
alt_allele_in_normal information no information from tumor sample.Any help would be great