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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:  

      /xchip/gdac_data/cptac3/genomic_data_mirror/CPTAC3_WashU_hg38/UCEC/WXS_CNV_hg38_v1.0_20180809

    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 (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."

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