TARGET-GDC Initial Data Release

[jamesqo]

What?

This PR adds the initial batch of TARGET studies sourced from GDC using ISB-CGC BigQuery.

List of studies included (added to CRDC readme too):

• alal_target_gdc: TARGET-ALL-P3, Acute Lymphoblastic Leukemia - Phase III
• aml_target_gdc: TARGET-AML, Acute Myeloid Leukemia
• bll_target_gdc: TARGET-ALL-P2, Acute Lymphoblastic Leukemia - Phase II
• nbl_target_gdc: TARGET-NBL, Neuroblastoma
• os_target_gdc: TARGET-OS, Osteosarcoma
• wt_target_gdc: TARGET-WT, Wilms' Tumor

checks

For all pull requests:

• Passes validation

For a new study (in addition to above):

• Does study name and study ID follow our convention? e.g. Tumor_Type (Institue, Journal Year); brca_mskcc_2015
• Is the study meta data complete? e.g. pmid, citation
• Were all samples profiled with WES/WGS? If not, is gene panel file curated?
• Are oncotree codes of all samples curated; Cancer Type and Cancer Type Detailed needs to be added in addition to Oncotree Code
• Clinical sample and patient data with meta files.
• Mutations data with meta file.
• Is the study based on hg38? If so, is the reference_genome: hg38 option included in meta study.
• CNA data with meta files
• CNA segment data with meta files
• Expression data including z-scores with meta files
• Other genomic profiles with meta files
• Case-lists for all profiles.
• Perform sanity checks based on the items in the checklist
• Manual checking (Niki or JJ): Triage or private Portal link here