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  1. Just a reminder that PDC has issued an alpha of it's MVP release.  Would be nice to have more Broadies take a look.  Presently supports only CPTAC2 data.

  2. iCoMut:
    1. undergoing update for UCEC AWG
      1. FYI:  HG38 mutation calls underway by WashU (slated for 11/8 V2 freeze)
    2. waiting for Broad example data to add new proteomics tracks
  3. HG38:  progress, GDCtools config file needed
    1. CN data:  


    2. But what is more biologically important:  WGS for CN or HG38?

      1. Because at present only VCFs available for WGS CN data

      2. Feedback:  Mani says WES is fine for Broad PG pipeline

      3. Karl needs WGS for some of his investigatory work (non-canonical ORFs, from HLA), but that's not ready for prime time sharing with other PGDACs yet, so it doesn't impact our G-CDAP

  4. LUAD: new proteomic data "in progress," but in "new location" @ DCC:
    1. per this email exchange
    2. Changed from/to:

      1. 8_CPTAC3_Lung_Adeno_Carcinoma/LUAD_mzML/

      2. 8_CPTAC3_Lung_Adeno_Carcinoma/A_CPTAC3_hg38_CDAP/LUAD_mzML/

    3. Per Nathan: "The files under A_CPTAC3_hg38_CDAP represent the re-run of the CDAP
      analysis for files analyzed before the release of Broad's new
      RefSeq/hg38 protein sequence database and any new ones going forward."