Using IMPUTED genotype data from UK Biobank to generate PRS scores using PRSice

Does the PRSice-2 tool support working with imputed genotype data provided by UK Biobank as listed here: https://biobank.ctsu.ox.ac.uk/crystal/label.cgi?id=263 ?

prsice ukbiobank

• 1,059 views • link

updated 4.7 years ago by Sam

• written 4.7 years ago by Jenish •

1 answer

Yes, use --type bgen, but be warned, that can be slow.

• 0 views • link

written 4.7 years ago by Sam

More posts like this

Differentiate sequenced and imputed variants in BGEN files
written 2.7 years ago by user230613

Hi there! I have recently started working with UK Biobank data, particularly with the imputed BGEN files (for whoever has access to UK Biobank, the …
heterozygous SNV AB>0.15, heterozygous indel<0.20 in UKB-WES
written 4.7 years ago by Shicheng Guo

These gVCFs were joint genotyped using GLnexus (https://www.biorxiv.org/content/10.1101/572347v1) to create a single, unfiltered project-level VCF (pVCF). Genotype depth filters (SNV DP≥7, indel DP≥10) were applied …
Biobank HLA *IMP:02 imputation labels ( A_4027 ? A_4386 ? B_7020 ?)
written 4.8 years ago by Jak •

I'm trying to parse the HLA imputation data from UK BioBank data and it lists the allele label headers here https://biobank.ctsu.ox.ac.uk/crystal/refer.cgi?id=2182 I assumed the format …
What is the best QC to do on imputed UK Biobank data?
written 4.9 years ago by psyc_biostars •

I am receiving imputed data from UK Biobank to conduct a GWAS on. Previously I have carried out GWAS on genotype data, which I have …
PRSice-2 without Ref SNP ID
written 4.9 years ago by Jenish •

Does PRSice-2 support a base tile that has chromosome number/name and chromosome position instead of reference SNP ID in the base file? I'm trying to …
UK BioBank
written 4.9 years ago by rogerdavis2609 •

Hi, I have started working on UK Biobank and I am completely clueless about the data structure. Is there is a tutorial (apart from the …
Preparing Target Data
written 5.2 years ago by Jenish •

Hi! I have a PGS file with the weights for each of the variants for a specific disease, CAD. The goal is to now calculate …
Accessing UK Biobank genotype information via patient ID
written 6.2 years ago by kylec1729 •

How does one access UK biobank genotype information via patient ID? I have extracted SNPs from a gene of interest using PLINK in .bgen+.sample file …
What is the best GWAS software suitable for extremely large dataset? (ex. Plink, Hail, BGENIE....)
written 7.3 years ago by Kim6845 •

Hi, Biostars I am working with large genotype dataset for GWAS, especially UK Biobank dataset. It contains 93,095,623 autosomal SNPs on 50 million individuals. (recorded …
UK biobank HLA imputation data
written 7.7 years ago by aleph9999 •

I'm interested in HLA imputation results from UK biobank (which was created by HLA*IMP 2 algorithm) and I have registered to have the access of …