Hello,

We are evaluating alternative methods for detecting variant sites and when dealing with VarScan we are a little confused why it assumes the reference base when < 8 reads map to a given position? Seems as though it would be more conservative to not assume any base. In particular, it appears that even when <8 reads map and they are all consistent in having a base different than the reference that VarScan still assigns the reference base.

For example, below is a position within a pileup file that shows the reference state is G with 6 Cs mapping to it and VarScan called the position as G in the vcf file.

scf7180000000002|quiver 1701 G 6 CCccCc &*!!!0

Any insight would be greatly appreciated.

Thanks,
jamie