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Old 08-29-2010, 01:52 PM   #33
RNM
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Location: Aus

Join Date: Apr 2009
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I have got somewhat related question, how do I tweak gsMapper parameters in order to get the reads mapped without introducing gaps. I am looking for SNPs and InDels and the gsMapper output (454AllDiffs.txt) shows gaps rather than mismatches. The mappings to the reference sequence looks fine, but when it comes to detecting variants the mapper is not doing what I expected it to do. Is there some extra step that I am missing for SNP/Indel detection? I have also tried AVA, but as my sequence is not an amplicon (far too big than the standard definition of amplicon in 454 terms), AVA isnt of much help either.
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