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Developed by
Thomas Abeel
TU Delft, formerly Broad Institute and VIB - Ghent University
Contributors
Thomas Van Parys, VIB
Marijn Vandevoorde
David Roldán Martínez
Where did the pileup/SNP track go with my BAM file?
Thu, 01/27/2011 - 01:25 — Thomas Abeel
Full question:
I wonder how I can display the pileup/SNP track. In an older version of GenomeView that I was using, when I was loading a BAMfile with short reads I was getting a SNP track but not anymore.
Answer:
In a recent version of GenomeView (1255+) we had to split the functionality of the pileup/SNP track and the short read track which shows the individual reads.
Essentially, the pileup was calculated in real-time, but this proved to be impractical for very large data sets. Therefore we now support the pile-up format from samtools, which has the pile-up and SNP functionality.
The pile-up track is described GUI section in the manual.
Details on how to prepare your data can found in the data preparation section of the manual.
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