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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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Does this work for VCFs with more than one trio? #30

Closed leipzig closed 9 years ago

leipzig commented 9 years ago

How can it annotate inheritance patterns on the variant level, as opposed to the individual level, if they differ between families?

moonso commented 9 years ago

Guess that when there are different families one would suspect different causing variants, maybe in the same gene but not same position. I'm working on a multi family analysis expansion to check this. If you really suspect the same variant in different families you can pretend that all individuals are in the same family by using the same family id for all individuals you have (and keep the other pedigree information intact) in the ped file and run it through genmod. You think that would work?

leipzig commented 9 years ago

No, the VCFs we use are over 1000 individuals wide. I think the point being that the annotation should be attributed to the probands, not to the variant.

moonso commented 9 years ago

Ok, we think of it as the annotation for this position in this family(one family per vcf). But I can try to make it suit your needs. How would you like to make the annotation in the analysis that you describe? Would it be a INFO field in the vcf like: GeneticModels = fam_1: AR_hom, fam_2: AD, fam_3: None, fam_4: AR_comp ...?

leipzig commented 9 years ago

Yes that work work. thanks

moonso commented 9 years ago

You can try this new feature out in this branch. Please give some feedback if you have time. I have not pushed to master yet since it needs some changing to the other genmod tools.

moonso commented 9 years ago

This is now standard in version 1.8.