Dear TCGA Colleagues,

The October 2012 Firehose analysis run has been uploaded and will be available in
the protected data tree pending internal mirroring by the DCC.  This analysis
run was based upon version 2012_10_24 of the Firehose stddata package, and is
described in more detail on our site at

			http://gdac.broadinstitute.org

The highlights of this run are given below and in the dashboard release notes.
If you have any questions or comments please do not hesitate to send them to
our gdac@broadinstitute.org mailing list.


Regards,
Michael S. Noble
Broad Institute of MIT & Harvard

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* More than 3000 new samples ingested; total of 475 analysis reports generated
* Sample differences:

  BCR          +171 (7123 total)
  Clinical     +119 (5798 total)
  CN           +398 (6212 total)
  LowP         +23  (501 total)
  Methylation  +882 (6471 total)
  mRNA         +1   (2225 total)
  mRNAseq      +808 (4371 total)
  miRseq       +851 (5644 total)
  MAF          +323 (3183 total)

* Internally this was a big release: every pipeline was rewired to accommodate
  use of sample sets of tumors, or normals, or type-specific subsets of each

* But that should in principle be transparent to external viewers: i.e. normals
  added as of stddata__2012_10_24 are NOT YET REFLECTED  in Firehose analyses
  (because very few analyses employ them at present)

* MutSig (v2.0) has been updated to restore the clustered mutations result

* Correlate_Methylation_vs_mRNA task was fixed to restore probe information
  removed in previous run

* Two enhancements to samples summary report available on our dashboard:

  - Now lists every sample that is filtered from the datastream, with an
    explanation of why (as per our online FAQ)

  - Heatmaps are now included that display available samples per data
    type vs. participants

* firehose_get v0.3.8: support additional awg runs, e.g. awg_thca__2012_10_24
  and awg_luad__2012_11_15