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BRCAChallenge / brca-exchange

Overall management and deployment of the BRCA Exchange web portal and pipeline scripts
http://brcaexchange.org
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Discrepancies between columns in built_with_change_types.tsv and rows in built_with_change_types.dictionary.tsv #1141

Open melissacline opened 4 years ago

melissacline commented 4 years ago
  1. It looks like the dictionary contains entries for the gnomAD hemizyous counts (e.g. Allele_count_hemi_exome_AMR_GnomAD) but the build file doesn't contain these counts.
  2. There appears to be a mis-edit on the line that contains the gnomAD NFE exome allele frequency: "Allele_count_hemi_exome_FIN_GnomADAllele_frequency_exome_NFE_GnomAD Allele Frequency in exomes of Finnish Populations".
  3. Additionally, the dictionary contains an entry for Consequence_GnomAD, which is not in the build file
  4. The dictionary is missing an entry for HGVS_GnomAD, which is in the build file.
  5. The dictionary still contains entries for pyhgvs_hg36_Start and _End fields. Low-impact. These issues should be fixed, but there's no need to hold up the release schedule.
melissacline commented 4 years ago

Update: 3, 4 and 5 seem spurious. Fixing 1 and 2.