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Old 03-29-2011, 08:22 AM   #1
rudi283
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Location: europe

Join Date: Sep 2010
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Default coverage and SNP detection

Hi,

I was wondering if there is a standard rule about coverage and SNP detection. How many reads (paired end) do I need to be able to say that's a SNP. I heard that need to be above 30 but I'm a bit confused. Does that mean that if I've got for example 15 I can't say it's a SNP?
I was wondering as wel if I can say it's a SNP when for example all forward reads have the change but non of the reverse reads (reads in pairs)- what does it mean?
The same if for example coverage is 60 but the reads are only from the same direction-reads from the other direction don't reach that point. Can I say it's a SNP?

Please help
Thanks!
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