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Old 03-18-2009, 10:17 PM   #1
hersh
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Location: india

Join Date: Feb 2009
Posts: 9
Default Coverage issue

I have a small query regarding the whole genome re-sequencing of a human genome using SOLiD system from ABI. We have very little amount of DNA and we are able to only make 2 mate pair libraries form it(25 microgram each). Our main interest is to detect genetic variations. We are planning to run 4 slides from one library,pulling it form 8 ePCRs(we will club 2 ePCR products to make one slide) so that we utilize maximum number of beads. We are expecting 8x-10x coverage after running both the libraries. Now I would like to know, is is sufficient coverage to determine true variants and other variation like indel? If it is sufficient coverage what is suggested threshold to call SNPs?
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