I am just now exploring the indel pipeline for SOLiD. Of course this has only recently been released. Unfortunately I am obtaining very few results. My understanding is that the pairing pipeline is suppose to produce a '*.pas' file that would contain possible indels. Then the indel pipeline takes this and produces the true indels. For some reason the pairing pipelines is creating very small '*.pas' files -- no more than 4 lines per chromosome and often less. Additionally the 'PAIR_INDEL_*.sh' command is running very quickly. No errors are showing up (e.g., out of disk space, etc.) and thus I am wondering what is happening. Any ideas would be appreciated.
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