I'm struggling with making VarScan's output adhere to GATK's strict rules for VCF files. Currently, I cannot understand what is wrong with this line:
1 20571284 . CAAAAAAA,AAAAAAAA C .
GATK says this cannot be parsed. Are two reference alleles not allowed, or is is supposed to be formatted otherwise?
EDIT: OK, what is the reference base at 20571284? Is it C or A or M or N?