Feature #520
closedColumns needed in latest-flat.tsv
Description
We should get the following fields in latest-flat.tsv so we can update gff_getevidence_map.py to use it instead of MySQL. (It's useful to include so the genome report can display allele frequency.):
allele_frequency.num
allele_frequency.denom
qualityscore_penetrance
Consider removing:
qualitycomment_in_silico
qualitycomment_in_vitro
qualitycomment_case_control
qualitycomment_familial
qualitycomment_severity
qualitycomment_treatability
For what it's worth (in case you're thinking about removing other columns), the columns I think gff_getevidence_map.py will use, in addition to the above that are needed, are:
['gene', 'aa_change_short', 'summary_short', 'impact', 'inheritance', 'dbsnp_id', 'qualityscore_in_silico', 'qualityscore_in_vitro', 'qualityscore_case_control', 'qualityscore_familial', 'qualityscore_severity', 'qualityscore_treatability', 'in_omim', 'in_gwas', 'in_pharmgkb', 'genetests_testable', 'genetests_reviewed']