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download tab is missing eventInfo for SV data

Open tmazor opened this issue 2 years ago • 3 comments

patients 36, 47, 58 show '-' or 'antisense fusion' but should show the gene partners as they do in prod

prod: image

beta: image

https://beta.cbioportal.org/results/download?cancer_study_list=msk_impact_2017&tab_index=tab_visualize&case_set_id=msk_impact_2017_all&Action=Submit&gene_list=TMPRSS2%250AERG%250AEGFR%250AEWSR1%250AALK%250ABRAF%250AROS1%250AEML4&show_samples=true&plots_horz_selection=%7B%22dataType%22%3A%22COPY_NUMBER_ALTERATION%22%2C%22selectedDataSourceOption%22%3A%22cna%22%2C%22mutationCountBy%22%3A%22MutationType%22%2C%22structuralVariantCountBy%22%3A%22MutatedVsWildType%22%2C%22logScale%22%3A%22false%22%7D&plots_vert_selection=%7B%22dataType%22%3A%22STRUCTURAL_VARIANT%22%2C%22selectedDataSourceOption%22%3A%22structural_variants%22%2C%22mutationCountBy%22%3A%22MutationType%22%2C%22structuralVariantCountBy%22%3A%22MutatedVsWildType%22%2C%22logScale%22%3A%22false%22%7D&plots_coloring_selection=%7B%7D&mutations_gene=EML4&comparison_subtab=alterations&comparison_selectedEnrichmentEventTypes=%5B%22structural_variant%22%5D

tmazor avatar Jun 22 '22 21:06 tmazor

same issue in Downloadable Data Files / Structural Variants: STUDY_ID SAMPLE_ID TMPRSS2 ERG EGFR EWSR1 ALK BRAF ROS1 EML4 msk_impact_2017 P-0000004-T01-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000015-T01-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000023-T01-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000024-T01-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000025-T02-IM5 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000025-T01-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000026-T01-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000027-T01-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000030-T01-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000034-T01-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000036-T01-IM3 NA NA NA NP NA NA Antisense fusion NP msk_impact_2017 P-0000037-T01-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000037-T02-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000039-T01-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000041-T01-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000042-T01-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000043-T02-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000047-T01-IM3 NA NA NA NP NA NA - NP msk_impact_2017 P-0000053-T01-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000055-T01-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000056-T01-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000057-T01-IM3 NA NA NA NP NA NA NA NP msk_impact_2017 P-0000058-T01-IM3 NA NA NA NP - NA NA NP

tmazor avatar Jun 22 '22 21:06 tmazor

@sbabyanusha this got overlooked when we released.
There are some SVs with eventInfo of type "Antisense fusion" and others with "ROS1-TMEM181 Fusion". Where they used to be the same in the old fusion data.

alisman avatar Aug 30 '22 22:08 alisman

@sbabyanusha reports that data will normalized in second release of SV data, at which point this issue should be resolved.

alisman avatar Aug 30 '22 22:08 alisman

@tmazor appears fixed in production

alisman avatar Jan 10 '23 17:01 alisman