Separating and determining alleles?

[michael-steffen]

Is there a way to separate and determine alleles with illumina paired end reads data? Essentially, what I want to do it replicate cloning without actually having to clone.

I have access to clc genomic workbench, and preferably would like to use this program.

Thanks,
Mike

[sarvidsson]

See my answer to your duplicate thread. I habe CLC as well as free tools, but don't like their viewer to perform such tasks - I find it easier to see the sequence pairs (and their connections) and the variant positions with IGV or Tablet.