genotype calling in gatk
After calling the genotype using Haplotyper Caller in gatk, i manually check the reads covering the variant sites. But i found one exception: The genotype of one sample was 0/0，wild type,but the reads for this site were .,,,..,,c.,c.c,.cccc. I think almost all the reads should be . or ,. Is this case normal?
Many thanks in advance!