Entering edit mode
9.9 years ago
897598644
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100
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!
What were their phred scores?
So what is their cutoff values?