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Old 05-31-2012, 10:36 AM   #1
lg36
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Location: london

Join Date: Mar 2012
Posts: 12
Default Please Help - SNP Calling in relation to Consensus Sequence Quality

Dear All,

I've posted on this before and attracted no interest at all. So I'd be very grateful to get your opinions. I'm relatively new to NGS sequence analysis so apologies for any naive assumptions.

As I understand (perhaps misunderstand) if a SNP is deemed to be present (after all the applied SNP filters, scores etc) then (most of the time) it will appear in the consensus sequence???

Is it therefore right to think if the consensus sequence is of a 'higher quality', the SNP's too will be of a 'higher quality'??

I'm defining quality of the consensus by the ability to reflect the presence or absence of certain oligonucleotides that we know to be there from PCR studies in the lab.

What I'm doing at the moment is trying to set the parameters correctly (paired end width, etc) in order to reach a consensus sequence that is correct according to what we know in the lab. Then I was planning on calling the SNPs based on the mapped reads we used for the best consensus sequence. Is there any validity at all in this approach, or are the two things SNP calling and consensus sequence production too 'unlinked' to make it invalid????

Many thanks in advance, apologies for any misconceptions

lg36
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