Open pnrobinson opened 5 years ago
(from Jules) The Exomiser API is very simple:
Pedigree probandOnly = Pedigree justProband(String id);
Pedigree fromFile = PedFiles.readPedigree(pedPath);
And you can validate it against a VCF like this:
String probandSampleName = “proband”;
Pedigree pedigree = PedFiles.readPedigree(pedPath);
VCFHeader vcfHeader = VcfFiles.readVcfHeader(vcfPath);
List<String> sampleNames = vcfHeader.getGenotypeSamples();
SampleIdentifier probandSample = SampleIdentifierUtil.createProbandIdentifier(probandSampleName, sampleNames);
Pedigree validatedPedigree = PedigreeSampleValidator.validate(pedigree, probandSample, sampleNames);
The InheritanceModeAnnotator uses the Jannovar API to do the analysis.
Two options -- hard filter (remove variants that do not cosgegregate as in PhenIX) -- make this a LR test. If the variant is disease related its probability is 1, and if not, it is the probability it would have cosegregated by chance, roughly similar to a lod score. Probaby the first option is sufficient for now