I have a question refering the field Reads supporting ALT (AD) in TCGA files.
I have used Annovar for annotation and I obtained lines like that:
line175 nonsynonymous SNV PRDM16:NM_022114:exon11:c.G2734C:p.A912P,PRDM16:NM_199454:exon11:c.G2734C:p.A912P, 1 3334434 3334434 G C hom 1 3334434 . G C 1 mf1 DP=280;MQ0=0;SOMATIC;SS=Somatic;VT=SNP; VLSC=. GT:AD:DP:FA:MQ0:BQ:SS:SSC 0/0:172,7:179:0.039:0:13:2:. 0/1:97,4:101:0.040:0:17:2:.
There is 0/0 in the normal column is associated with the SS=2, SS=Somatic, which means, there is a mutation in the tumor but the AD field for tumor is 97,4, which means 97 reads for the reference allele and 4 reads for the alternative allele. Shouldn't it be a 0/0 instead a 0/1?
Is there something wrong with the annotation or am I misunderstanding these fields?
Thanks for your support!
