-- DBMS: bigquery
CREATE TABLE `isb-cgc-bq.pancancer_atlas.Filtered_MC3_MAF_V5_one_per_tumor_sample`
(
  ParticipantBarcode STRING OPTIONS(description="TCGA barcode identifier for the study participant, eg TCGA-02-0001"),
  Tumor_SampleBarcode STRING OPTIONS(description="Original TCGA tumor sample barcode.TCGA-WC-A885-01A, TCGA-HQ-A2OF-01A."),
  Tumor_AliquotBarcode STRING OPTIONS(description="Original TCGA tumor aliquote barcode. Examples: TCGA-WC-A885-01A,TCGA-XF-AAN3-01A"),
  Normal_SampleBarcode STRING OPTIONS(description="Sample Barcode For The Normal Tissue. Examples: TCGA-V4-A9EI-10A, TCGA-V4-A9EI-10A"),
  Normal_AliquotBarcode STRING OPTIONS(description="Aliquot Barcode For The Normal Tissue. Examples: TCGA-CR-7385-10A-01D-2013-08, TCGA-DX-A3M1-10A-01D-A22A-09"),
  Normal_SampleTypeLetterCode STRING OPTIONS(description="Sample Type Letter Code. The subset of 4 values currently used are: NBC, NB, NT, NBM. See https://Gdc.Cancer.Gov/Resources-Tcga-Users/Tcga-Code-Tables/Sample-Type-Codes"),
  Study STRING OPTIONS(description="TCGA study abbreviation, eg LAML. Full list available at https://gdc.cancer.gov/resources-tcga-users/tcga-code-tables/tcga-study-abbreviations"),
  Hugo_Symbol STRING OPTIONS(description="HUGO symbol for the gene (HUGO symbols are always in all caps). \"Unknown\" is used for regions that do not correspond to a gene"),
  HGVSp_Short STRING OPTIONS(description="Protein sequence of the variant in HGVS recommended format, but using 1-letter amino-acid codes. \"p.=\" signifies no change in the protein"),
  Variant_Classification STRING OPTIONS(description="Translational effect of variant allele; eg. Missense_Mutation, Nonsense_Mutation, etc."),
  HGVSc STRING OPTIONS(description="The coding sequence of the variant in HGVS recommended format"),
  CENTERS STRING OPTIONS(description="One or more genome sequencing center reporting the variant"),
  FILTER STRING OPTIONS(description="List of failed filters (if any), or \"PASS\" indicating the variant has passed all filters.")
)
OPTIONS(
  friendly_name="PanCancer Filtered Merged MAF",
  description="Extracted from the PanCancer Atlas initiative on the GDC in Sept 2016 (file name pancan.merged.v0.2.5.filtered.maf.gz). Contains Somatic mutation calls.    \n\nNote: Data was filtered such that the only rows with the Variant_Classification in {Frame_Shift_Del, Frame_Shift_Ins, In_Frame_Del, In_Frame_Ins, Missense_Mutation, Nonsense_Mutation, Nonstop_Mutation, Splice_Site, Translation_Start_Site} were retained (Consistent with e.g. ISB, MSKCC, Broad definition of mutated gene). Moreover, Additional annotations were added (e.g. ParticipantBarcode). FPPP project aliquots were removed, and Rows with a solid tissue normal reference were removed if a corresponding blood derived normal reference was available.   \n\nMore details https://gdc.cancer.gov/about-data/publications/PanCan-MYC-2018",
  labels=[("category", "processed_-omics_data"), ("status", "current"), ("access", "open"), ("source_0", "gdc"), ("data_type", "somatic_mutation"), ("program", "pancancer_atlas"), ("reference_genome", "hg19"), ("source_1", "literature")]
);

INSERT INTO `isb-cgc-bq.pancancer_atlas.Filtered_MC3_MAF_V5_one_per_tumor_sample` (ParticipantBarcode, Tumor_SampleBarcode, Tumor_AliquotBarcode, Normal_SampleBarcode, Normal_AliquotBarcode, Normal_SampleTypeLetterCode, Study, Hugo_Symbol, HGVSp_Short, Variant_Classification, HGVSc, CENTERS, FILTER) VALUES ('TCGA-04-1331', 'TCGA-04-1331-01A', 'TCGA-04-1331-01A-01W-0486-08', 'TCGA-04-1331-10A', 'TCGA-04-1331-10A-01W-0486-08', 'NB', 'OV', 'ZNF728', 'p.A320S', 'Missense_Mutation', 'c.958G>T', 'SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS', 'wga'), ('TCGA-04-1331', 'TCGA-04-1331-01A', 'TCGA-04-1331-01A-01W-0486-08', 'TCGA-04-1331-10A', 'TCGA-04-1331-10A-01W-0486-08', 'NB', 'OV', 'FAM166A', 'p.P140A', 'Missense_Mutation', 'c.418C>G', 'SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS', 'wga'), ('TCGA-04-1331', 'TCGA-04-1331-01A', 'TCGA-04-1331-01A-01W-0486-08', 'TCGA-04-1331-10A', 'TCGA-04-1331-10A-01W-0486-08', 'NB', 'OV', 'CLDN9', 'p.D76H', 'Missense_Mutation', 'c.226G>C', 'SOMATICSNIPER|VARSCANS', 'wga'), ('TCGA-04-1331', 'TCGA-04-1331-01A', 'TCGA-04-1331-01A-01W-0486-08', 'TCGA-04-1331-10A', 'TCGA-04-1331-10A-01W-0486-08', 'NB', 'OV', 'CABIN1', 'p.T2200R', 'Missense_Mutation', 'c.6599C>G', 'SOMATICSNIPER|VARSCANS', 'wga'), ('TCGA-04-1331', 'TCGA-04-1331-01A', 'TCGA-04-1331-01A-01W-0486-08', 'TCGA-04-1331-10A', 'TCGA-04-1331-10A-01W-0486-08', 'NB', 'OV', 'BRCA2', 'p.C711*', 'Nonsense_Mutation', 'c.2133C>A', 'SOMATICSNIPER|RADIA|MUTECT|MUSE|VARSCANS', 'wga');