Tag: SAIGE

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…

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SAIGE GWAS – error – samples in geno file do not have phenotypes

SAIGE GWAS – error – samples in geno file do not have phenotypes 0 Hey, so I have this error when running step 1 of saige with a subset of my plink files, and pheno file, following the tutorial from github.com/weizhouUMICH/SAIGE/ Error:: 5685 samples in geno file do not have…

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Adjusting for common variant polygenic scores improves yield in rare variant association analyses

Taliun, D. et al. Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. Nature 590, 290–299 (2021). Article  CAS  PubMed  PubMed Central  Google Scholar  Szustakowski, J. D. et al. Advancing human genetics research and drug discovery through exome sequencing of the UK Biobank. Nat. Genet. 53, 942–948 (2021). Article …

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Bioinformatics Programmer II – Hybrid/Remote

#119126 Bioinformatics Programmer II – Hybrid/Remote Extended Deadline: Tue 2/21/2023 This position will remain open until a successful candidate has been identified. UCSD Layoff from Career Appointment: Apply by 10/03/2022 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 10/13/2022….

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Bioinformatics Programmer II – Hybrid/Remote – 119126 at UC San Diego Health System

This position will remain open until a successful candidate has been identified. UCSD Layoff from Career Appointment: Apply by 10/03/2022 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 10/13/2022. Eligible Special Selection clients should contact their Disability Counselor for…

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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…

Continue Reading Why may BOLT-LMM and SAIGE (quantitative, linear-mixed model) yield different results when ran on the absolutely the same dataset?