Tag: bgen

How do I restrict to only hm3 SNPs for plink analyses? 0 Hello! I am trying to use plink to select only hm3 snps from the ukb bgen files that I have, but I am at a total loss as to how to proceed. I am really new to all…

Hi there, I have two separate sets of gwas data (‘A’ and ‘B’) with a file per chr.  I am running a targeted gene/pathway analysis so I have filtered out snps per each gene location (209 snps = 209 filtered gene-specific files). For dataset A I ran the following commands:…

how to convert bcf files into bgen 0 Hi guys, I downloaded vcf.gz files (22 per each chromosome) from TopMed after imputation. Then, I filtered my vcf.gz files per MAF through bcftools, which gave me in output files in bcf format. I am wondering: there is a tool being able…

Hi,   I have been using the newest version of PLINK2 (www.cog-genomics.org/plink/2.0/) to perform a sex-SNP interaction analysis with a binary outcome.     I ran the following command:   plink2 –bgen [FILE].bgen –sample [FILE].sample –pheno-name [pheno] –covar [FILE].phen –covar-name sex PC1 PC2 PC3 PC4 PC5 PC6 PC7 PC8 PC9…

plink2 bgen to vcf ukbiobank 2 Hello I have imputed data from ukbiobank in bgen format. I would like to convert it to a vcf file. I can use plink2 to make pgen files and then use plink2 again to create a vcf plink2 –bgen ukb_imp_chr17_v3.bgen –sample ukimp_chr17_v3_s.sample –make-pgen plink2…

I have a BGEN file that I obtained from a PGEN file via PLINK2. The command I used is as follows: plink2 –pfile my_file –export bgen-1.2 bits=8 –out /some/path –output-chr chrM and I used hl.index_bgen() to create an idx2 index. Now when I have the BGEN file and the idx2…

Hi everyone, I am currently preprocessing UK Biobank genetic data in order to run a GWAS. I am working with the imputed data, which I transformed to .pgen files and then merged into a single file containing all chromosomes. I have run into a problem with excluding variants with poor…

How can I keep INFO value when convert bgen to VCF by using plink2? 1 I am working on file handling for GWAS. When I converted bgen to VCF by using plink2 with a commands below, all INFO (and also FILTER) columns became “.” in the output VCF files. A…

Using QCTOOL v2 to process UK Biobank .bgen files – why so slow? 0 I’m currently using QCTOOL v2 to process imputed .bgen files from UK Biobank, however they seem to be processing very slowly. Is this normal? My command is pretty basic; I’m filtering out a list of SNPs…

Hi, I am trying to merge two bgen files using qctool as explained here. I am using qctool_v2.2.0. The command works but ends with an error: ❱ qctool -g bug/in2.bgen -s bug/in2.sample -merge-in bug/in1.bgen bug/in1.sample -og bla.bgen -os bla.sample Welcome to qctool (version: 2.2.0, revision: unknown) (C) 2009-2020 University of…

P-values far too high for quantitative regenie phenotype 0 Hi all, I’m having some trouble running regenie (v2.2.4) on a quantitative phenotype for a large cohort. I’m testing a standard height GWAS with heights rounded to the nearest integer. I’ve tried a few different tests to see where the issue…

Hi all, I have a vcf file that was extracted from UKB data using qctool (v2.0.6-Ubuntu16.04-x86_64) and contains data in the GP format. This contains a bunch of SNPs from a single chromosome. ❱ wc -l chromosome1.vcf 260 chromosome1.vcf Then I try to convert this file to .bgen again using…

As a validation experiment, I have run the same GWAS of a quantitative phenotype derived from the UKBiobank, alongside the genomic data from the UKBiobank, once using the program BOLT-LMM and once using SAIGE linear mixed model (with selected quantitative trait tag). I wanted to see if the results would…

formatting error: Calculate LD matrix from bgen file 1 Hello, I am new to plink and am learning as I go. I am trying to calculate an LD matrix for a list of variants while using a bgen file as my reference population. See the command below: ./plink2/plink2 –r2 bin…

extract list of SNPs from multiple chr{1:22}.bgen files using plink2 1 hello, I have extracted out list of snps based on the maf cutoff 0,,0.0001, 0.001,0.01,0.1,.55,1.0. I am running plink2 to extract this list from .bgen files for individual chromosomes using the following code plink2 –chr{1:22}.bgen –extract maf1_snps for imputed…