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Old 05-29-2013, 04:11 AM   #1
lre1234
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Location: US

Join Date: Aug 2011
Posts: 105
Default Same sample - multiple lanes

Hi all,
I am doing some whole genomes. Each sample (2 samples, so 24 lanes in total) was run using 12 lanes of a solid5500 machine. for the post-sequence analysis, I have aligned each lane individually, and my question is this:

Is it better to merge all 12 of the individual alignments together and then do the indel realign and base reaclibration on 1 large file? I have been trying this, but I can't seem to get through the base-recalibration step as the program fails due to an error of not having enough memory.

Or can I do the indel realign and base reaclibration on each individually aligned lane, and then merge everything together after all of this is complete?

I suspect that option 1 is the best approach but probably computationally the most expensive. Any thoughts would be appreciated.
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