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Old 01-22-2010, 12:25 PM   #2
jjohnson
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Location: Washington DC Metro Area

Join Date: Aug 2009
Posts: 20
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Hi Ha,

The mapper application uses a combo of flow signals info quality scores, and difference type information to determine if a variant is of high quality. The HCDiffs file contains variants that have at least 3 non-duplicate reads relative to the reference or to other reads at that specific location.

I also found another thread that discusses uppercase and lower case and maybe helpful.

http://seqanswers.com/forums/showthread.php?t=1948
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