Opened 2 months ago
Last modified 26 hours ago
#1575 new task
Impute genotypes from OncoArray data
Reported by: | Nicklas Nordborg | Owned by: | Nicklas Nordborg |
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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...
Change History (27)
comment:1 by , 2 months ago
comment:6 by , 2 months ago
In 7604:
References #1575: Impute genotypes from OncoArray data
Implemented the phasing step with ShapeIT. Since the program is not so good at multi-threading, we start one process per chromosome instead limited to the number of assigned threads. The wrapper code is very similar to the code in the WGS variant calling. A full run takes ~1.5 hour to complete this step (using 8 threads).
In 7599: