difg_glass_2019: GLASS consortium study

[rmadupuri]

Fix #933

Data Source:
Synapse: https://www.synapse.org/#!Synapse:syn17038081/wiki/585622. The data available here represents the second release of the GLASS dataset as of 2019-03-28.

Data Summary:
288 patients (not just the gold set of 222 patients as mentioned in Nature paper).
710 aliquots from 586 samples (EXCLUDING the Normal blood/tissue samples).

Data Schema:
https://www.synapse.org/#!Synapse:syn17038081/wiki/585706

Data conversion from synapse to portal format (for future reference):
1. Patient Level: clinical.cases, clinical.surgeries, Paper Supp Table1, Supp Table7
2. Sample Level: biospecimen.samples, biospecimen.sample_types, biospecimen.aliquots, clinical.surgeries, Paper Supp Table8
3. MAF: variants.passgeno, variants.anno, variant.variant_classifications, biospecimen.aliquots

• passgeno table contains the variants that passed all filters. No reference allele info in the table.
• anno table contains funcotator and VEP annotations for each variant in the passgeno table independent of sample-level information. ~9000 variants in passgeno table are not present in anno table. Final variant count 13,562,066
• After mapping to samples table, and removing the normal sample variants (~4,091,230), the final variant count is 9,470,836.

4. Expression:
5. Methylation:
6. Segment:

[stale]

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