[DOCKTESTERS] Broad PCAWG Tokens definition?

[Gordon Saksena]

The tokens task is part of the PoN (Panel of Normals) filter.  It is a Java
program that collects stats on the Normal BAM for the current donor.  These
stats are later aggregated with stats from the other samples (in another
docker), and then used to flag certain variants in a VCF as suspect (in a
third docker).  The overall algorithm is in the process of being published.


It should be one of the more straightforward algorithms to test - it has
very predictable CPU time and RAM usage, and should produce outputs that
can be tested via an exact binary match.  It accepts just the normal BAM
for its input.

I'm planning later dockers to have a similar structure, though with
increased memory and core requirements.  The .wdl file will continue to
contain a single task, with the bulk of the pipeline wiring embedded inside
the docker.  The dockers will either accept the source BAMs (for callers)
or VCFs (for filters) as inputs.  If you have feedback I can incorporate it
into the other dockers.

Gordon

On Thu, Oct 20, 2016 at 4:08 PM, Alexander Buchanan <buchanae at ohsu.edu>
wrote:

> Hey Gordon,
>
>
>
> I’m new here so maybe I missed this, but what is the tokens task? How
> would you describe what it does and the results it produces?
>
>
>
> Thanks!
>
> Alex Buchanan
>
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