prior.somatic
Prior probabilities for somatic mutations. First value is for
the case when no matched normals are available and the variant is not in
dbSNP (second value). Third value is for variants with MuTect somatic call.
Different from 1, because somatic mutations in segments of copy number 0
have 0 probability and artifacts can thus have dramatic influence on
likelihood score. Forth value is for variants not labeled as somatic by
MuTect. Last two values are optional, if vcf contains a flag Cosmic.CNT,
it will set the prior probability for variants with CNT > 2 to the first
of those values in case of no matched normal available (0.95 default).
Final value is for the case that variant is in both dbSNP and COSMIC > 2.