I would like to be able to replicate what Galaxy does to find indels on
my own machine. However, I am facing the following challenges:
1. I want to find Indels in the 3-way multiz alignment of hg18,
panTro2, and rheMac2, but I cannot find the alignment anywhere. Where
can I get the alignment file?
2. I cannot find code for extracting the Indel's anywhere. What
program did you use?
Thanks so much!
Irene
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