The gemini query tool allows querying by variant and the inheritance tools described above enable querying by gene for fixed inheritance patterns. The gene_wise tool allows querying by gene with custom genotype filters to bridge the gap between these tools.
gemini gene_wise $db --min-filters 3 --gt-filter "gt_types.fam1_kid == HET and gt_types.fam1_mom == HOM_REF and gt_types.fam1_dad == HOM_REF" --gt-filter "gt_types.fam2_kid == HET" --gt-filter "gt_types.fam3_kid == HET" --columns "chrom,start,end,gene,impact,impact_severity" --filter "max_aaf_all < 0.005"
--gt-filter
allows one to specify filters to apply to the returned rows.
--show-samples
Finding out which samples have a variant.
-show-families
Finding out which families have a variant.
--sample-delim
Changing the sample list delimiter
--format
Reporting query output in an alternate format.
--carrier-summary-by-phenotype Summarize carrier status