Can graphtyper be used to genotype cancer samples ?

DecodeGenetics / graphtyper

Population-scale genotyping using pangenome graphs

http://dx.doi.org/10.1038/ng.3964

MIT License

164 stars 20 forks source link

Can graphtyper be used to genotype cancer samples ? #87

Open rbr7 opened 3 years ago

rbr7 commented 3 years ago

Hi,

i have a query wrt to the tool and its utility in genotyping cancer samples ?

what model does it assume in genotyping, is it diploid model ?

Can somatic SVs for tumor samples be used to genotype accurately using graphtyper ?

Thanks

hannespetur commented 3 years ago

Hello, yes only diploid genotyping model is available and we don't have any guidelines for genotyping somatic SVs. You could discover the somatic SVs with Manta and then call them using graphtyper but you'd need to find a way to determine the final genotyping from the read counts/support.

Best, Hannes