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

Join Date: Aug 2010
Posts: 39
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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
http://sourceforge.net/apps/mediawik...?title=SAM_FAQ

Will that do the trick?
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