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Old 01-31-2011, 01:39 PM   #2
Location: Heidelberg, Germany

Join Date: Aug 2010
Posts: 39

My recommendation would be to align the reads to your reference using the long read option in BWA or Lastz (or something else with long read capacity) and output a SAM file. You should be able to get SNPs out of the SAM file pretty easily following the SAM Tools FAQ here

Will that do the trick?
dagarfield is offline   Reply With Quote