Changes between Initial Version and Version 28 of Ticket #1575


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Timestamp:
Apr 29, 2024, 9:58:32 AM (3 weeks ago)
Author:
Nicklas Nordborg
Comment:

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  • Ticket #1575 – Description

    initial v28  
    22
    33We 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.
     4
     5**Update** We decided to use Beagle instead. See https://faculty.washington.edu/browning/beagle/beagle.html
     6
    47
    58Reference files can be downloaded from:
    … …  
    710https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/1000G_2504_high_coverage/working/20220422_3202_phased_SNV_INDEL_SV/
    811
    9 Once we have the imputed genotypes we can use them to calculate a Polygenic Risc Score (PRS). See other ticket to be created...
     12**Update** This reference data set doesn't include all variants that we need for the PRS313 calculation. Instead we will use the Phase3 reference: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ and convert it to hg38.
     13
     14Once we have the imputed genotypes we can use them to calculate a Polygenic Risc Score (PRS). See other ticket #1576.