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Old 11-29-2011, 09:06 AM   #2
Senior Member
Location: Sweden

Join Date: Mar 2008
Posts: 324

I had the same problem, my solution was to change the mapping quality. This issue is supposed to be fixed in the latest version of BFAST, so an better option would be to realign reads with mapQV 255. Or just use Samtools mpileup.
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