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Old 03-16-2011, 03:20 AM   #1
Oxygen81
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Location: Germany

Join Date: Aug 2009
Posts: 11
Question Maq SNPfilter

Hello everyone,

I used Maqs SNP filter with the default settings. If I got it right SNPs with a consensus quality (fourth column) < 20 will be discarded. But the output looks like that:
226980 T C 63 23 1.00 63 62 Y 235 T
238765 C A 229 95 1.00 63 62 M 137 C
318701 T C 5 13 1.00 63 60 Y 171 T
352302 G A 223 65 1.00 63 62 N 154 N

Has someone else observed something like that and could explain what happened? Please tell me if I have made a mistake with my thinking.

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