Dear TCGA Colleagues,

The July 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_07_25 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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New Samples:
    BCR         +160    (6846 total)
    Clinical    + 55    (5633 total)
    Methylation +140    (5465 total)
    mRNAseq     +306    (3460 total)
    miRseq      +195    (3976 total)

New Reports:
    32 more reports, for a total of 284 in this run

New Pipelines:
    Correlate_Clinical_vs_CopyNumber_Focal
    Correlate_Clinical_vs_CopyNumber_Arm

MutSig:
    Added stick figures
    To address item (9) from 2012_06_23 Analysis Run Release Notes, input WIGs
       (from stddata__2012_07_25) updated to hg19 for:
            BLCA BRCA CESC KIRC LUSC LUAD PRAD STAD UCEC

    STAD failing due to memory exhaustion - ignoring, as there is no active AWG

Gistic2
    Failed for PANCANCER due to memory exhaustion; ignored because it is the
    large 23-tumor cohort, not (yet) the 8-tumor cohort defined by AWG