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Clinical-Genomics / genmod

Annotate models of genetic inheritance patterns in variant files (vcf files)
http://moonso.github.io/genmod/
MIT License
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Some variants without GeneticModels annotation #93

Closed geocarvalho closed 4 years ago

geocarvalho commented 4 years ago

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  .
moonso commented 4 years ago

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!