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I am aligning Illumina paired end sequence using BWA, then run SAM-to-BAM
resulting in a 1.1 Gb file.

But when I then generate pileup on this file column 4 (consensus bases) are all
N's and the file is now 8.4 Gb.

Can someone tell me what might be going on?

Any help much appreciated.


Alison Gardner

Neurogenetics Research Program,
SA Pathology (at Women's and Children's Hospital),
Level 9, Clarence Rieger Bldg.,
72 King William Road, North Adelaide,
S.A., Australia, 5006

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