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titleFirehose 2013_02_22 Analysis Run
  • Sample changes since last analyses 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 describe and reflect custom Firehose runs for TCGA 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:
    • CoMut plot inconsistency for MutSig 2.0 results
      • The CoMut plot was generated using a Q threshold of 0.5 (0.1 was used in previous runs)
      • Many more genes are displayed in the plot due to this change
      • This change was inadvertent and the Q threshold will be reverted to 0.1 in the next analyses run
    • MutSigCV introduced (MutSig2N is deprecated, and will be removed next month)
    • MutSig is now compatible with WashU WIG files
    • MutSigPreprocess now more configurable has Firehose native task (no longer GenePattern)
      • Bug fixed that only manifests in certain cases, and only when there are WGS+capture MAFs for some of the same patients
    • GenerateStickFigures* DCC submission archive removed: its content rolled into general Mutsig DCC 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 in 2.0.17 where output file "raw_copy_number.pdf" was being named "[pathname '.pdf']"
    • CopyNumber_GeneBySample removed (was only for hg18; its output has been superseded by GISTIC)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
  • Output of cluster aggregator Aggregate_Molecular_Subtype_Clusters now packaged for DCC submission:
    • Provides a table of patient vs. clusterings (per datatype, per clustering method)
    • Where each cell indicates the respective patient membership in that given cluster group

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

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