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mimi_lupton 10-31-2008 09:48 AM

Maq SNP calls from a large pool
Hi there,
I am carrying out a candidate gene re-sequencing project where I have run PCR products from a large pool of individuals (311 people) on Solexa. This means I have a very high depth of sequence reads (as much as 2000) to try and get SNP calls out of. If possible it would be great if anyone has any advice on using Maq to analysis this data. I have managed to run an easyrun and can view my alignments in Maq view. I am trying to play around with the different easy run options to get SNP calls that make sense.


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