Update docs on custom namespaces and cna long format #9924

BasLee · 2022-12-07T12:21:23Z

Update File Formats documentation on:

new CNA long format
custom namespace columns for CNA and structural variants

Luke-Sikina

Just some cleanup - thanks for the docs!

docs/File-Formats.md

Luke-Sikina · 2022-12-07T19:40:29Z

docs/File-Formats.md

-
-Note: namespace columns are recognized by a case-insensitive match of the namespace reported in the mutations meta file
-and the first word in the column header.
+Additional mutation annotation columns can be added to the cBioPortal mutation data file. In this way, the portal will parse and store your own MAF fields in the database. For example, mutation data that you find on cBioPortal.org comes from MAF files that have been further enriched with information from [mutationassessor.org](https://mutationassessor.org/), which leads to a "Mutation Assessor" column in the [mutation table](https://www.cbioportal.org/index.do?cancer_study_list=acc_tcga&cancer_study_id=acc_tcga&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=acc_tcga_mutations&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&data_priority=0&case_set_id=acc_tcga_sequenced&case_ids=&patient_case_select=sample&gene_set_choice=user-defined-list&gene_list=ZFPM1&clinical_param_selection=null&tab_index=tab_visualize&Action=Submit).
