I have paired samples of tumor, and normal. I have identified germline mutations from normal sample, and somatic mutations from the pair.
Now, I would like to run ContEst on both tumor and normal samples.
It seems to be straightforward for normal sample. B:genotype,vcf should be the germline mutation vcf file.
Should it be ok if my vcf file has germline mutations for all normal samples that include the normal sample for which I am doing contamination estimate?
But what value should I give to this parameter B:genotype,vcf for contamination estimate for tumor sample?