Dear TCGA Colleagues,

The Feb 2013 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 2013_02_22 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.
Finally, note that in addition to our standard monthly data and analysis runs
we are also providing custom runs targeted to specific AWG needs (as discussed
below)

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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- Sample Changes since last analysis run:

	BCR			-8		(7460 total)
	Clinical	+158	(6107 total)
	CN			+304	(6856 total)
	LowP		+35		(636 total)
	MAF			+266	(4200 total)
	Methylation	+141	(6759 total)
	miRseq		+433	(6060 total)
	mRNAseq		+228	(5018 total)

- Increased number of output reports from 614 to 703

- New AWG Analyses:
	. New pages added on NCI wiki and Broad GDAC site to reflect custom Firehose runs for analysis working groups
	. Performed and/or released custom AWG runs for LGG, LUAD, GBM, PANCAN12, and THCA

- New Correlation Analyses (see Nozzle reports in dashboard for more info):
	Correlate_molecularSubtype_vs_CopyNumber_Arm
	Correlate_molecularSubtype_vs_CopyNumber_Focal
	Correlate_molecularSubtype_vs_Mutation

- Mutation Analyses:
	MutSigCV introduced (MutSig2N is deprecated, and will be removed next month)
	MutSig is now compatible with WashU WIG files
	MutSigPreprocess now more configurable as FH native task (not GenePattern)
	Fixed bug that manifests only when there are WGS+capture MAFs for some patients
	GenerateStickFigures* DCC submission archive removed: now in Mutsig archive

- Copy Number Analyses
	GISTIC now more configurable as Firehose native task (no longer GenePattern)
	Updated to version 2.0.17a:
	memory and performance optimization of peak identification code. 
	SegArray version 1.06 with Mex files added to improve performance. 
	Fix gistic_plots chromosome shading for q-value 0.
	Fix bug where raw_copy_number.pdf output file was named "[pathname '.pdf']"
	CopyNumber_GeneBySample removed (was only for hg18; superseded by GISTIC)

- Pathway Analyses:
	Now in their own "Pathway Analyses" section of top-level aggregate reports
	(instead of catch-all "Other" section)
	Restored clarity of pathway analysis task names & output archives:
		Pathway_Paradigm_mRNA
		Pathway_Paradigm_mRNA_And_Copy_Number
		Pathway_Paradigm_RNASeq
		Pathway_Paradigm_RNASeq_And_Copy_Number
		Pathway_Hotnet
	This changes the name of their respective DCC submission archives

- Aggregate_Molecular_Subtype_Clusters pipeline now packaged for DCC submission:
	Provides table of patient vs clusterings (per datatype, per cluster method)
	Where each cell indicates the respective patient membership in given cluster

- General Software Tools:
	firehose_get v0.3.11 released
	The internal gdac_freeze tool can now input a custom sample set, to facilitate
	efficiently analyzing cancer subtypes