$ gemini de_novo --columns "chrom, start, end, ref, alt" test.de_novo.db --min-kindreds 1 --gt-pl-max 1000 | cols
chrom start end ref alt gene variant_id family_id family_members family_genotypes affected_samples family_count
chr10 48003991 48003992 C T ASAH2C variant_id:2 2 2_dad(dad;unaffected),2_mom(mom;unaffected),2_kid(child;affected) C/C,C/C,C/T 2_kid 2
chr10 48004991 48004992 C T ASAH2C variant_id:3 3 3_dad(dad;unaffected),3_mom(mom;unaffected),3_kid(child;affected) C/C,C/C,C/T 3_kid 2
chr10 135336655 135336656 G A SPRN variant_id:4 2 2_dad(dad;unaffected),2_mom(mom;unaffected),2_kid(child;affected) G/G,G/G,G/A 2_kid 2
chr10 135336655 135336656 G A SPRN variant_id:4 1 1_dad(dad;unaffected),1_mom(mom;unaffected),1_kid(child;affected) G/G,G/G,G/A 1_kid 2
chr10 135369531 135369532 T C SYCE1 variant_id:5 1 1_dad(dad;unaffected),1_mom(mom;unaffected),1_kid(child;affected) T/T,T/T,T/C 1_kid 3
chr10 135369531 135369532 T C SYCE1 variant_id:5 2 2_dad(dad;unaffected),2_mom(mom;unaffected),2_kid(child;affected) T/T,T/T,T/C 2_kid 3
chr10 135369531 135369532 T C SYCE1 variant_id:5 3 3_dad(dad;unaffected),3_mom(mom;unaffected),3_kid(child;affected) T/T,T/T,T/C 3_kid 3
chr10 1142207 1142208 T C WDR37 variant_id:1 1 1_dad(dad;unaffected),1_mom(mom;unaffected),1_kid(child;affected) T/T,T/T,T/C 1_kid 1
with multiple affecteds, it looks like:
$ gemini autosomal_dominant --columns "chrom, start, end, ref, alt, impact, impact_severity" test.auto_dom.db | cols
chrom start end ref alt impact impact_severity gene variant_id family_id family_members family_genotypes affected_samples family_count
chr10 48003991 48003992 C T non_syn_coding MED ASAH2C variant_id:3 2 2_dad(dad;unaffected),2_mom(mom;affected),2_kid(child;affected) C/C,C/T,C/T 2_mom,2_kid 4
chr10 48003991 48003992 C T non_syn_coding MED ASAH2C variant_id:3 3 3_dad(dad;affected),3_mom(mom;unknown),3_kid(child;affected) C/T,C/C,C/T 3_dad,3_kid 4
chr10 48004991 48004992 C T non_syn_coding MED ASAH2C variant_id:4 3 3_dad(dad;affected),3_mom(mom;unknown),3_kid(child;affected) C/T,C/C,C/T 3_dad,3_kid 4
chr10 48004991 48004992 C T non_syn_coding MED ASAH2C variant_id:4 2 2_dad(dad;unaffected),2_mom(mom;affected),2_kid(child;affected) C/C,C/T,C/T 2_mom,2_kid 4
chr10 135336655 135336656 G A intron LOW SPRN variant_id:5 3 3_dad(dad;affected),3_mom(mom;unknown),3_kid(child;affected) G/A,G/G,G/A 3_dad,3_kid 1
chr10 1142207 1142208 T C stop_loss HIGH WDR37 variant_id:1 3 3_dad(dad;affected),3_mom(mom;unknown),3_kid(child;affected) T/C,T/T,T/C 3_dad,3_kid 2
chr10 1142207 1142208 T C stop_loss HIGH WDR37 variant_id:1 2 2_dad(dad;unaffected),2_mom(mom;affected),2_kid(child;affected) T/T,T/C,T/C 2_mom,2_kid 2```
Looking good! What is the purpose of repeating "variant_id:" in each row? Also, I think affected_samples should just be samples, as the variants may be present in individuals who are not affected with a phenotype, so this will avoid confusion.