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Old 07-01-2015, 02:52 AM   #4
Linnea
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Location: Uppsala, Sweden

Join Date: Mar 2010
Posts: 23
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No sorry, I can't explain that part, maybe someone else has an idea?

But actually, why can't they just be real indels with a very high quality? (99 seems to be the highest quality you can get: "Because the most likely PL is always 0, GQ = second highest PL - 0. If the second most likely PL is greater than 99, we still assign a GQ of 99, so the highest value of GQ is 99." -from the GATK webpage). Maybe it will be clear after the realignment? (And sorry if I misunderstood something, I am really no indel expert..)
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