Find SNP in Sanger sequenced gene

[genelab]

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!

[dagarfield]

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/mediawiki/samtools/index.php?title=SAM_FAQ

Will that do the trick?

[shayeste]

hello everyone
I am a new member