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mskcc / pluto-cwl

CWL workflows for helix filter scripts
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Make data_mutations_uncalled and meta_mutations_uncalled files for cBioPortal #63

Open stevekm opened 3 years ago

stevekm commented 3 years ago

Need to update the samples fillout worklflow to create data_mutations_uncalled.txt and meta_mutations_uncalled.txt files

might be able to bundle it into this script; https://github.com/mskcc/helix_filters_01/blob/master/bin/update_fillout_maf.py

@timosong

timosong commented 3 years ago

Requirements for data_mutations_uncalled.txt For any row where t_alt_count== 0, set Mutation_Statusto UNCALLED, and place in file called data_mutations_uncalled.txt These rows are mutually exclusive to data_mutations_extended.txt.

Requirements for meta_mutations_uncalled.txt File format is similar to this: https://github.com/cBioPortal/datahub/pull/1418/files#diff-54c74f8a4d51dd53d8b56d293f21f02f78c035a9dded8928b957de3a3ae72c64 Only variable line is: cancer_study_identifier: glioma_msk_2018 This should be the name of the study id

timosong commented 2 years ago

@stevekm This filter requirement must be extended to not only t_alt_count == 0 but also: If fillout == True then place mutation row in data_mutations_uncalled.txt regardless of depth.