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Old 07-01-2015, 03:46 AM   #5
Zaag
Senior Member
 
Location: Amsterdam

Join Date: Nov 2009
Posts: 112
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GQ does not tell you anything about the variant quality. GQ tells you about how certain the HC is about the zygosity.

About the deletions: do they disappear if you use this option in the variant calling step?

--dontUseSoftClippedBases
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