Robert Sheridan

When variants are submitted for annotation in GenomicLocation format, the Reference Allele is always present. But genome-nexus also provides api endpoint "/annotation" which accepts alleles in HGVS format. This format...

common allele suffixes should be trimmed from requests

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NotationConverter.normalizeGenomicLocation(GenomicLocation genomicLocation) will strip a common nucleotide prefix from a Genomic Location, removing invariant nucleotides at the start of the variant from the variant representation. (e.g. "AG -> AT" becomes...

A presumed recent change in the response schema from myvariant.info caused a failure to enrich some variants submitted to the annotation endpoints of genome-nexus. However, this failure occurred silently and...

remove unneeded references to old tables

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Describe changes proposed in this pull request: - tables pdb_uniprot_alignment and pdb_uniprot_residue_mapping were removed at db version 2.12.12 there is no need to refer to them in cgds.sql or cgds-h2.sql...

Support of negative value entrez_gene_id genes in clickhouse table development

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Some production databases at MSK, and also if users set up their database with microrna support, or if any phosphorylated genes are added as gene records, then negative values will...

Additional review needed for the identification of WGS/WES samples in clickhouse table development

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This relates to cases where a study contains a sample which appears to be part of a genetic profile, but the sample is not present in data_gene_matrix.txt, or the gene...

Clarification needed on how to handle missing gene panel identifiers in data files

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This relates to cases where a study contains a sample which appears to be part of a genetic profile, but the sample is not present in data_gene_matrix.txt, or the gene...

This branch adapts the cBioPortal production codebase for direct use with a ClickHouse deployed database. This is to demonstrate and explore the feasibility of eliminating the mySQL dependency entirely as...

When attempting to Visualize 3D Structure from the mutations tab of the results page, the 3d molecular model pdb file fails to be downloaded from the rcsd pdb website. Browser...