Hi, I work with sequencing populations of viruses. Quite often, we get mixtures of bases, such as G or T = K. We are currently using phred and our own program to assemble and call the mixtures. What we would like to do is to use phred and phrap for aligning and assembly, and then use the Staden package to find and annotate the mixtures. Does the staden package have this kind of functionallity? If so, could someone explain how to do this and maybe point me to a document describing how Staden identifies these mixtures?
There's limited support for such things. What is there works reasonably well, but heteorzygous detection is not being actively worked on at the moment.
See http://staden.sourceforge.net/mutations/index.html for some discussion on the topic.
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