Originally posted by maivantan
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But are you sure that those results make sense? Samtools should be telling you what the reference letter is at each point, but in your output, they are all N's. I suggest you search this site for when other people have had that problem, and attempt to fix that.
That problem is why you have no 0/0 results; if your reference letters are all N's, you will never have homozygous matches.
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