AnnotationDB Integration Required Mods Bugs - NIAGADS/GenomicsDBWebsite GitHub Wiki

EGA Modified .tsx/.ts files

  • MostSevereConsequences.tsx -- probably no additional mods needed at this time

    • updated to reflect new attribute names and types
    • layout altered

  • types.ts -- cleanup still needed

    • updated to add/remove VariantRecordAttributes
    • clean up still needed for this and other record attributes (probably should wait until other record types are fixed)
    • updated GeneRecordAttributes

  • VariantRecordHeading.tsx -- probably no additional mods needed at this time

    • removed references to removed attributes
    • refactored layout, especially ADSPQCDisplay component

  • GeneRecordHeading.tsx

    • updated attribute names for genetic evidence for ad flags
    • commented out embeded igv browser

Website Bugs?! / Needed Fixes

  • record visible (as defined in individuals.txt) attributes are assumed to be tables and throw an error precluding page load

    • e.g., cadd_phred_score -- currently set to record-internal in individuals.txt to allow page load; will need to alter that to record to debug

  • Record Tables

    • "No variants meet the default p-value cutoff for genome-wide significance..." when you filter on text phrase that is not matched; not sure if that is the behavior we want; should discuss (fixed in 15f82d4)
    • inline bar-charts (e.g., allele frequencies) -- switch the colors, making the lighter one the values -- (fixed in initial branch integration)

  • Motif Consequences table rendering error

    • see: app/record/variant/1:68742147:A:G_rs542665189#motif_consequences

    uncaught Error: Objects are not valid as a React child (found: object with keys {icon, type, color, value}). If you meant to render a collection of children, use an array instead.`

`in div (created by TdComponent)`
`in TdComponent (created by ReactTable)`
`in div (created by TrComponent)`
`in TrComponent (created by ReactTable)`
`in div (created by TrGroupComponent)`
`in TrGroupComponent (created by ReactTable)`
`in div (created by Tbody)

 * problem may be related to `motif_score_change`; uncertain
 **UPDATE:** it seems to be a problem with the attribute type, which right now is set to `numeric` but, judging by the payload, should be `json_icon` -CK
  • Transcript Consequences table on Variant Page
    • Coding? check is not showing (this is probably an issue in the query)
    • results are supposed to be ordered by rank ASC; check qeury

DB Bugs / Need Fixes

  • Tuning Indexes

    • to speed up LocusZoom GWASService: Results.VariantGWAS on protocol_app_node_id, 'chr' || split_part(variant_record_primary_key, ':',1)::text, and possibly position

  • NIAGADS.Variant

    • sequence alleles for deletions may be wrong b/c length check was based on alt instead of norm alt. corrected in VariantAnnotator PERL lib and in real-time generated alleles from AnnotatedVDB, need to patch db (both sequence and display alleles)
      • can possible use display_allele_attributes('GTTT','TT', 'GT', 'T',196994570) SQL function to facilitate patching

  • Missing SRes.ExternalDatabases

    • need to add in external datatabase to the GenomicsDB for gnomAD and ESP so can join on version for allele frequency table

  • AnnotatedVDB

    • ea/aa in allele frequencies are not from 1000genomes but from NHLBI-Exome Sequencing Project (ESP)

      • patch AnnotationDB by iterating over and fixing allele_frequencies field
      • correct loading scripts
      • will need to update website queries, which currently correct the error in real-time

    • update loading scripts to do lookups of internal Ensembl motif ids (motif regulatory consequences) during load so do not have to require storage of huge motif database (current solution)

  • Future review

    • NHGRI GWAS SNP x SNP interactions from the NHGRI GWAS catalog (currently skipped)