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dnanexus / UKB_RAP

Access share reviewed code & Jupyter Notebooks for use on the UK Biobank (UKBB) Research Application Platform. Includes resources from DNAnexus webinars, online trainings and workshops.
MIT License
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No need to liftover to Hg38 #31

Closed nshrine closed 6 months ago

nshrine commented 7 months ago

On this page: https://github.com/dnanexus/UKB_RAP/tree/main/end_to_end_gwas_phewas/liftover_plink_beds_tmp It says: "In order to perform association testing with the sequncing data on step-2, it is required to get the array genotyping data on the same reference coordinate as the sequencing data."

Whereas it seems it is actually not required but simply desirable: https://github.com/rgcgithub/regenie/issues/82

Arkarachai commented 7 months ago

Yes, I confirm this is correct based on discussion with Regenie developer. Mainly we try to avoid translocation among different version. However, we will clarify this to avoid confusion. @oklempir-cf

anastazie-dnanexus commented 6 months ago

Thank you for catching this, I edited README by saying that it is desirable and added link to regenies discussion.