pileup

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

Answer: 

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?

Answer: 

For general instructions on preparing the pileup format
http://genomeview.org/content/preparing-pileup

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

We typically end up with something like:
bigfile.bam.swig.bgz

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

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.

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