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Old 01-30-2011, 09:41 PM   #1
genelab
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Location: honston

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Default Find SNP in Sanger sequenced gene

Hi guys,
I have about 120 sequences of the same genes from our sample, which are sequenced by Sanger methods, How can I get the SNP sites among this gene compared to the reference gene? Is there any software can help me do this?

Any sugestion will be highly appreciated!
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Old 01-31-2011, 01:39 PM   #2
dagarfield
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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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Old 03-10-2014, 11:35 PM   #3
shayeste
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hello everyone
I am a new member
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