genotype calling in gatk

Excuse me:

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!

Answers

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