Add more sample-level information for display in cBioPortal

[ckandoth]

Add more columns to data_clinical.txt, using http://oncotree.mskcc.org/cdd/api/ to standardize column names if possible.

• MOUSE_CONTAMINATION - For batches with at least 1 PDX sample, report fraction of sequenced reads that align to mouse genome.
• PROJECT_CODE - IGO request ID. E.g. Proj_08392_B
• FACETS_PLOIDY, FACETS_PURITY, FACETS_WGD, FACETS_VERSION if available.
• FRACTION_GENOME_ALTERED - fraction of Genome CN altered from FACETS results.
• MUTATION_COUNT - Number of mutations from analysis MAF.
• NONSYNONYMOUS_MUTATION_COUNT - Number of mutations from portal MAF.
• DNA_INPUT - value in input_ng from sample_patient.txt file
• LIBRARY_YIELD - value in Library_yield from sample_patient.txt file
• PIPELINE_VERSION - version number of pipeline
• PIPELINE - name of analysis pipeline used

[timosong]

PMs requesting to have DNA_INPUT, LIBRARY_YIELD, IGO_ID, MOUSE_CONTAMINATION hidden in cbioportal.

should we add TMB?

[ckandoth]

@timosong You should be able to control which fields are exposed/hidden by default. Lookup "cBioPortal file formats". For TMB, we have a separate GitHub ticket. Don't implement that now.