Consensus sequence/ positional nucleotide summary in IGV

vl80

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Consensus sequence/ positional nucleotide summary in IGV

04-01-2013, 05:14 PM

Is it possible to obtain a positional nucleotide summary and a consensus sequence using IGV? I am using IGV to visualise an alignment done usine Miseq reporter. My aim is not to identify mutations, but just to obtain a sequence and then BLAST that. Length of the reference genome is only 70K but the matches are at pactchy locations, I tried the feature area of interest in IGV to see however failed to find a way to download a consensus sequence.
Thanks a lot.
PS - I am using the Java based GUI not run commands.
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