View Single Post
Old 12-14-2011, 09:11 AM   #5
Senior Member
Location: San Diego

Join Date: May 2008
Posts: 912

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.
swbarnes2 is offline   Reply With Quote