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Old 12-05-2011, 06:23 PM   #2
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Location: St. Louis

Join Date: Dec 2010
Posts: 535

With 75x coverage and I'm assuming paired end reads that has a size distribution with a standard deviation of at least 30bp, it is very unlikely for you to get multiple reads to pile up at the same exact locations without them being PCR duplicates. I would remove them for SNP calling.
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