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Old 09-28-2009, 01:16 PM   #192
apfejes
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Location: Oakland, California

Join Date: Feb 2008
Posts: 236
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Hi kmcarr - thanks for the clarification. I was under the impression that Gerald was simply one step in the process, rather than a wrapper around the Eland calls. It's getting harder and harder to keep on top of all of the different aligner formats and pipelines.

For the record, I rarely use Eland output of any form myself. We mainly use Maq here and I expect we'll be moving to SAM/BAM based formats in the future.
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