First of all, sorry if this is a very naive question but I could not find the answer in the user's manual of SomaticSniper . Question: why there are some reported variants in the VCF output of SomaticSniper in lowercase? What does that mean?
#CHROM POS ID REF ALT QUAL FILTER INFO ... 1 575876 . G C . . . 1 821143 . g T . . . 1 825104 . g A . . .