Is there any way to make sure that the vertical scales for multiple sequencing lanes match in the pile up track?


Goto 'File'> 'Configuration' > 'Pile up tracks'

Set the maximum height to whatever you want it to be.

What extension should the tab-delimited pileup have?


For general instructions on preparing the pileup format

For the tab delimited file, you should include .swig somewhere in the filename.

We typically end up with something like:

Where did the pileup/SNP track go with my BAM file?


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.

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