genotype calling in gatk

Excuse me:

After calling the genotype with 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!

alignment sequence next-gen-sequencing genome

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updated 4.4 years ago by Ram

• written 11.6 years ago by 897598644

What were their phred scores?

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updated 4.4 years ago by Ram

• written 11.6 years ago by Devon Ryan

So what is their cutoff values?

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updated 4.4 years ago by Ram

• written 11.6 years ago by 897598644

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