Categories
Tag: BOLT-LMM
Identification of constrained sequence elements across 239 primate genomes
De novo assembly and repeat-masking To maximize the species diversity of primates in our analyses, we newly sequenced and assembled the genomes of 187 different primate species, initially presented in refs. 11,23, for which no other reference genome assembly was available. In brief, each individual was sequenced with 150 bp paired…
A versatile, fast and unbiased method for estimation of gene-by-environment interaction effects on biobank-scale datasets
UK Biobank The UK Biobank is a large population-based study which includes over 500,000 participants living in the United Kingdom41,42 (www.ukbiobank.ac.uk/). Men and women aged 40–69 years were recruited between 2006 and 2010, and extensive phenotypic and genotypic data were collected. Quality control of genotype data was applied for individual…
A genome-wide association study of blood cell morphology identifies cellular proteins implicated in disease aetiology
INTERVAL study The INTERVAL study was a randomised trial of approximately 45,000 blood donors aged eighteen years or older who were recruited at 25 NHSBT (National Health Service Blood and Transplant) static donor centres across England21. The study was approved by the Cambridge East Research Ethics Committee and we complied…
PLINK format file for BOLT-LMM
PLINK format file for BOLT-LMM 0 I would like to perform BOLT-LMM to assess the association of SNP with a quantitative trait. BOLT-LMM requires PLINK format files (bed, bim, fam) and imputed files (bgen, sample). Should I use direct genotype data typed from SNP arrays for the plink format files?…
LD score table for East Asians used for BOLT-LMM
LD score table for East Asians used for BOLT-LMM 0 I would like to use BOLT-LMM to analyze SNP data of East Asians. The BOLT-LMM requires a table of reference LD scores appropriate for the target ancestry. The LDSC site has various files calculated from 1000 genomes East Asians. (console.cloud.google.com/storage/browser/broad-alkesgroup-public-requester-pays)…
Assistance Needed with Converting VCF File for BOLT-LMM Usage
Assistance Needed with Converting VCF File for BOLT-LMM Usage 0 Dear PLINK Community, I hope this message finds you well. I have encountered a challenge while attempting to convert a VCF file into a format suitable for association analyses using BOLT-LMM. Despite several days of effort, I have been unable…
Biobank-scale inference of ancestral recombination graphs enables genealogical analysis of complex traits
ARG-Needle and ASMC-clust algorithms We introduce two algorithms to construct the ARG of a set of samples, called ARG-Needle and ASMC-clust. Both approaches leverage output from the ASMC algorithm11, which takes as input a pair of genotyping array or sequencing samples and outputs a posterior distribution of the TMRCA across…
Why may BOLT-LMM and SAIGE (quantitative, linear-mixed model) yield different results when ran on the absolutely the same dataset?
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…