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Old 12-14-2011, 12:28 PM   #6
Location: Netherlands

Join Date: Dec 2009
Posts: 13

Originally Posted by swbarnes2 View Post
Illumina reads are error prone. If you pull every single read with a discrepancy from reference, you are going to pull a lot of noise.

I don't think that a pileup can be generated with only variant positions, but you could grep the pileup to only get lines with alterante letters. The pileup will have the position, all the letters called by all the reads that cross the position, and all the qualities for all the reads that cross the position.
Yes, but how can I run a pileup on a single position with 500 million X coverage ? I think i will need to do this read by read...
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