Opened 9 months ago
Last modified 7 months ago
#1575 closed task
Impute genotypes from OncoArray data — at Initial Version
| Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
|---|---|---|---|
| Priority: | major | Milestone: | Reggie v4.54 |
| Component: | net.sf.basedb.reggie | Keywords: | |
| Cc: |
Description
We have some samples which have been genotyped on the OncoArray platform. It should be possible to implement an analysis that impute genotypes for a lot more positions.
We have already made some tests with Shapeit5 (https://odelaneau.github.io/shapeit5/) and Impute5 (https://jmarchini.org/software/#impute-5) which seems to be working well.
Reference files can be downloaded from: https://github.com/odelaneau/shapeit4/tree/master/maps and https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/
Once we have the imputed genotypes we can use them to calculate a Polygenic Risc Score (PRS). See other ticket to be created...
