Where the short BAMs are
This is not a question, but a tip. It might be common knowledge, but well, if you're a bit on your own as we are, you might not know this (our Institute's bioinformatician found this info when she started using the standalone TVC).
As you all know, each exome downloaded from the main run results page are about ~30GB in size each, because they contain flow information.
However, running the VariantCaller plugin is by default performed with the option `--postprocessed-bam "..."`. The postprocessed BAM does not include flow data, and reads have been trimmed of primer sequences.
These postprocessed BAM files, which are around 7GB each, are perfectly fine for applications that do not use flow data, such as viewing the reads on IGV; and can be downloaded from each individual sample's VariantCaller plugin output page. That is: click on the sample name under the VariantCaller output, then download the "TVC-Processed Reads".