I am analyzing WES VCF files for tumor and matched non-tumor samples and noticed that the allele frequency (AF) values in the files are quite high for the variants (>0.5 and close to 1 for a lot of the variants). This was the case for the variants that I found were present only in the tumor sample but not in the non-tumor sample, so I assume that must mean that the variants/mutations I'm working with are somatic - right? The high allele frequency is what is worrying me a bit - is that normal? Is there another way I could confirm that these variants are somatic. I did not do the variant calling, it was done by the service provider and I'm told that they used GATK for variant calling. I've used SnpEff eff for variant annotation.
Apologies, this is the first time for me to work on this and I don't work with anyone who has expertise around me. Appreciate your help and patience.