Hello, thank you for your awesome work in genmod!
I'm would like to use it on some samples I have for a project, but some of the variants present in the multi VCF I'm using doesn't have the GeneticModels annotation, is this normal?
From the 1745 variants in the multi VCF, just 187 doesn't have this annotation.
Example without:
chr2 202082459 rs13006529 T A 2480.27 . ABHet=0.484;ABHom=1;AC=3;AF=0.5;AN=4;BaseQRankSum=-1.137;DB;DP=290;Dels=0;ExcessHet=3.0103;FS=0;HaplotypeScore=6.7127;MLEAC=1;MLEAF=0.5;MQ0=0;MQ=60;MQRankSum=0;OND=0;QD=10.68;ReadPosRankSum=1.172;SF=0,1;SOR=0.988;set=Unified;Annotation=CASP10GT:GQ:AD:PL:DP 0/1:99:76,81:1705,0,1473:157 1/1:99:0,133:3312,247,0:133
Example with:
chr1 10355834 rs3753037 C T 974.77 . ABHet=0.511;AC=1;AF=0.5;AN=2;BaseQRankSum=0.472;DB;DP=93;Dels=0;ExcessHet=3.0103;FS=0;HaplotypeScore=5.5623;MLEAC=1;MLEAF=0.5;MQ0=0;MQ=60;MQRankSum=0;OND=0;QD=10.6;ReadPosRankSum=0.66;SF=0;SOR=0.622;set=Unified;Annotation=RNU6-37P,KIF1B;GeneticModels=FAM01:AD;ModelScore=FAM01:99 GT:PL:AD:DP:GQ 0/1:1003,0,988:47,45:93:99 .
Hi @geocarvalho , sorry for not replying I had not seen this. Yes if a variant does not follow any genetic models they will not be annotated.
Good luck!
Hello, thank you for your awesome work in genmod! I'm would like to use it on some samples I have for a project, but some of the variants present in the multi VCF I'm using doesn't have the GeneticModels annotation, is this normal? From the 1745 variants in the multi VCF, just 187 doesn't have this annotation.
Example without:
Example with: