Tag: GWAS

michigan imputation server 0 Hi, I performed imputation on my GWAS data using Michigan imputation server. Now I have two output files: 1).dose.vcf.gz and 2).info.gz Michigan imputation server use mimimac3 (–format GT,DS,GP) and in the output file “.dose.vcf.gz” are present all the three formats. I’m new on this kind of…

michigan imputation server 0 Hi, I performed imputation on my GWAS data using Michigan imputation server. Now I have two output files: 1).dose.vcf.gz and 2).info.gz Michigan imputation server use mimimac3 (–format GT,DS,GP) and in the output file “.dose.vcf.gz” are present all the three formats. I’m new on this kind of…

Newest ‘gwas?page=2&sort=Newest&pageSize=50’ Questions – Bioinformatics Stack Exchange …

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Source: minimac4 Version: 1.0.2-3 X-Debbugs-CC: debian…@lists.debian.org Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of minimac4 the autopkgtest of minimac4 fails in testing when that autopkgtest is run with the binary packages of minimac4 from unstable. It passes when run with only packages from testing. In…

Source: minimac4 Version: 1.0.2-3 X-Debbugs-CC: debian…@lists.debian.org Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of minimac4 the autopkgtest of minimac4 fails in testing when that autopkgtest is run with the binary packages of minimac4 from unstable. It passes when run with only packages from testing. In…

How to classify the SNPs/gene loci as reported or novel? 1 I have a big list of significant SNPs (>30K) from a GWAS/meta-analysis. Can you please suggest what are some best ways to find the respective gene names and further classify them as already reported and novel ones? Thanks in…

I can get SHAPEIT to work with the default Plink PED/MAP format input files, but not with a VCF as input. As an example, here I use the demo data that comes with SHAPEIT, which runs well. DEMO=/Users/michaelflower/bin/shapeit.v2.904.3.10.0-693.11.6.el7.x86_64/example shapeit -B $DEMO/gwas.bed $DEMO/gwas.bim $DEMO/gwas.fam -M $DEMO/genetic_map.txt -O “$DIR”/shapeit/gwas.phased However, when I…

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How can get significant results from the GWAS summary statistics results 0 How can I use the GWAS summary statistics results and get the most significant genes and SNPs? summary GWAS PGS statistics • 41 views • link updated 47 minutes ago by gokberk ▴ 70 • written 2 hours…

Allele coding in BGENIE GWAS output 1 Hi all, I have a quick question about BGENIE GWAS summary stats. In the summary statistics, alleles are coded as a_0 and a_1, looks like as the following: chr rsid pos a_0 a_1 af info pheno1_beta pheno1_se pheno1_t … 22 22:16050075:A:G 16050075 A…

How to analyze genotype data and imputed data in GWAS study 0 Dear users, I am new to GWAS study, I have a concern about genetic association procedures. After having real genotyped data from the experiment ( we use the array for genotyping), we need to impute the genotype data….

Hello r/bioinformatics. I’m a student studying plant selection (with an interest in bioinformatics) and right now for a course work (yeah I know using reddit for homework is frowned upon) I need to showcase an example of GWAS used to identify biotic stress. So I found this example of GWAS…

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DOI: 10.18129/B9.bioc.cageminer     Candidate Gene Miner Bioconductor version: Release (3.14) This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users must define a set of guide genes, which are known genes involved in the studied phenotype. Additionally,…

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How to make .ped and .map files 0 Hello I have a dataset but I need to create .ped and .map files (as I understand) in order to use plink to run a GWAS. However, I do not know what files I need to use in order to create them,…

How to run a GWAS in command line with Plink2? 0 I am trying to run a GWAS in the command line with plink version 2, however when I run the following command plink2 –file hapmap1 I get the following error Error: Unrecognized flag (‘–file’) I am trying to follow…

Significance Some social insects exhibit split sex ratios, wherein a subset of colonies produce future queens and others produce males. This phenomenon spawned many influential theoretical studies and empirical tests, both of which have advanced our understanding of parent–offspring conflicts and the maintenance of cooperative breeding. However, previous studies assumed…

Polygenic scores in diabetic individuals across UKBB 1 Hi all, I am calculating PRS for a binary trait (T2D) across UKBB individuals. I am using external GWAS from PRS catalog in order to acquire weights for the base file. I have noticed the weights are given in the form of…

PLINK Dosage file without family ID error 0 Hi, I am simply trying to extract a small set of SNPs from a .dos dosage file using plink1.9. However, I get the error: Line 1 of yourfile.dos has fewer tokens than expected I have checked that the .fam file and the…

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GWAS – Relationship between Standard Error and P-value 1 Is there a relationship between the p-values obtained in a GWAS and the standard error of the effect size of a SNP that can that can be explained either explicitly or intuitively? Methods for prediction based on effect sizes, such as…

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Category Research / Academic Location Wageningen Do you want to use as researcher your expertise in analyses of whole genome sequences to contribute to research to identify functional genetic variants in pigs to improve genomic selection? Do you want to work together with national and international breeding organisations? We have…

The Senior Scientist operationally delivers client projects for Biomarker and Genomic Medicine (BGM) services. S/he demonstrates deep knowledge of scientific principles and concepts related to one or more capabilities and is experienced in industry standards. S/he will provide support for the BGM strategy and interpretation to other SBUs and clients….

Dutta RK, Larsson M, Arnesen T, Heie A, Walz M, Alesina P, Gimm O, Söderkvist P Sci Rep 11 (1) 10562 [2021-05-18; online 2021-05-18] Aldosterone-producing adenomas (APAs) are a major cause of primary aldosteronism (PA) and are characterized by constitutively producing aldosterone, which leads to hypertension. Several mutations have been…

Hi everyone, I am trying to munge some data for later use in ldsc and I come into this error: /home/expcard/Projects/GWAS_SCA/GWAS_NTR/LDSC/ldsc/munge_sumstats.py –sumstats /home/dominicz/LDSC/SCAMILIFELINESforMETALnoSNPFinalLDSCmunge.txt –N 18236 –chunksize 500000 –out /home/dominicz/LDSC/SCAMILIFELINESforMETALnoSNPFinalLDSC.munge.txt –merge-alleles /home/dominicz/LDSC/w_hm3.snplist LD Score Regression (LDSC) Version 1.0.1 (C) 2014-2019 Brendan Bulik-Sullivan and Hilary Finucane Broad Institute of MIT and Harvard…

Background: Intramuscular fat (IMF) content is a determining factor for meat taste. The Luchuan pig is a fat-type local breed in southern China that is famous for its desirable meat quality due to high IMF, however, the crossbred offspring of Luchuan sows and Duroc boars displayed within-population variation on meat…

deflated QQ plot but lambda >1 1 Dear All, What might be the reason for a deflated QQ-plot but lambda showing > 1 value. GWAS (case-control using glm-logistic regression adjusting for PC1-PC3 and three covariates) was done in plink2.0, and QQ plot using QQman package TIA package plink deflation GWAS…

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PLINK and population stratification with known subpopulations 0 I want to perform a genome wide association study (GWAS) with PLINK 1.9. I have whole genome sequencing SNP calls for ~100 patients where I know in advance that there is a skew towards subpopulations of African and South American descents, with…

How to check the allele strand of variants? 1 Hi all, I have a list of variants obtained from various GWAS studies, it is important for me that all variant alleles (alternate allele) located on the forward strand. Could you please kindly tell me how I can check this issue…

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Checking chromosome builds for genotyping data 0 Hi, I have several studies worth of data (In both PLINK and vcf format), and I was wondering if anyone knew of an online tool which I could use to check my chromosome build i.e GRCh37 vs GRCh38. (I thought I used one…

I’m about to begin revising the 14th edition of my human genetics textbook. In normal times, I’d have amassed technical articles and case reports, as well as notes from meetings and interviews, choosing topics to add or ax and updating or replacing examples as the new edition takes shape. But…

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The advent of technology making feasible elucidation of whole genomic sequencing over the past 30 years has led to reports of many if not most important or interesting animal genomes (including the most celebrated results of the Human Genome Project) (see, e.g., “Nautilus pompilius Genome Determined“; “Giraffe Genome Reveals Relevant…

Prader–Willi syndrome (PWS) is associated with a specific molecular signature — a set of genes that can be used as markers for a certain trait — in the brain that is linked to episodes of psychosis, or a loss of contact with reality, a mouse study found. According to the…

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How to make Q-Q plots for different models at a single chart using R? 1 Hello everyone! I am trying to make a Q-Q plot to visualise p-values obtained from different models afterr runing GWAS analysis. The key thing is that I want to reflect p-values from the different models…

Polygenic Risk Score Analysis for an individual genome 2 Hello, I am developing a model for PRS calculation. For PRS, you need the base data and target data. I have got these datasets however, it is not clear how the model can be used to predict the susceptibility of a…

GWAS Studies 0 How to create a .ped file for use in PLink? I have the following csv file: Chromosome Position Sample1 Sample 2 ……….. Sample n Chr Pos Sam1 Sam2 Sam3, Sam 4, ……Sample_n 1 11 A T T, A, A, T, …… 2 141 G G G, T,…

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GWAS data from PGC 0 this is my first time using the GWAS data, I downloaded some data from PGS and I Have some questions. 1- there are a lot of SNP to the same gene with different P-values, why does this occur? and if I want to use one…

How do I know the SNPS which are removed when clumping are in a LD block or SNPs not existed in 1000 Genome 0 Hi everyone, I’m not sure how to know why my SNPs are being removed applying clumping when reading the exposure data (in MR analysis). I would…

This article was originally published here J Neurooncol. 2021 Oct 20. doi: 10.1007/s11060-021-03878-5. Online ahead of print. ABSTRACT BACKGROUND: Risk factors for meningioma include female gender, African American race, high body mass index (BMI), and exposure to ionizing radiation. Although genome-wide association studies (GWAS) have identified two nuclear genome risk…

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Math behind association with PLINK 1 Hi, which is the mathematical formula behind the –linear association used by plink ? plink association gwas • 307 views The most basic association test is just a Chi-squared test on a 2 x 2 contingency table of the minor allele tallies, as to…

How long does it take to carry out the GWAS workflow? 0 Including these steps: 1) raw data format transformation for five companies 2) update positions for all SNPs to hg37 version 3) Quality control within companies 4) Pre-phasing (SHAPEIT2) and imputation (IMPUTE2) for all SNPs of each company 5)…

This article was originally published here Biochim Biophys Acta Mol Basis Dis. 2021 Oct 15:166291. doi: 10.1016/j.bbadis.2021.166291. Online ahead of print. ABSTRACT OBJECTIVES: To investigate in silico the presence of nucleotide sequence complementarity between the RNA genome of Severe Acute Respiratory Syndrome CoronaVirus-2 (SARS-CoV-2) and human non-coding (nc)RNA genes. METHODS:…

Labelling SNPs in a stacked manhattan plot with karyoploteR 0 When combining multiple GWAS results into a stacked manhattan plot using KaryoploteR, how do you label top SNPs in each set of GWAS results? Instructions provided for labelling a single manhattan plot did not work for the stacked manhattan. manhattan…

How do I merge imputed GWAS data 0 I have a cohort that part of the participants were genotyped using the Illumina 2.5M DNA microarray chip and another group of participants using H3Africa chip. I have imputed them using HRC server. To increase the power for my association analyses, I…

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Introduction Genome-wide association studies (GWASs) have brought enormous progress in mapping the genetic basis of common diseases or traits, 1 Visscher P.M. Wray N.R. Zhang Q. Sklar P. McCarthy M.I. Brown M.A. Yang J. 10 years of GWAS discovery: Biology, function, and translation. , 2 Claussnitzer M. Cho J.H. Collins…

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SNP-based heritability in GWAS (GREML) 0 Hello everyone, i am curious, if it is recommandable to estimate the heritability of a quantitative trait (where actually exact data are known) in a case-control study. Like i have 300 german shepard and i know exactly the length of the tongue of each…

Calculate z-scores from GWAS summary stats 2 Hello, I need to calculate the z-scores from meta-GWAS summary stats. The association file has the following header rs_id Allele1 Allele2 Freq1 Effect StdErr P.value The ‘effect’ is the Beta coefficent. My understanding is z-score=Effect/StdErr Is that correct ? Also, are there any…

Hello, there is an error when I try to filter a VCF document for MAF. Here is a part of the the vcf-file: 2: chr1H 523 chr1H:523 C A . PASS . GT 0|0 1: chr1H 445 chr1H:445 C T . PASS . GT 0| 2: chr1H 523 chr1H:523 C…

Calculating PRS in UK Biobank 0 Hi, I want to calculate PRS in UK Biobank with PRSice2. However, the GWAS used a lot of UK biobank participants as control and proxy case. They then ran a PRS on a cohort where the meta-analysis of the summary stats excluding the cohort…

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Hey everyone! I’m a new grad student in genetics and don’t remember college stats from undergrad and I don’t take research stats in grad school till next semester. I’m currently writing a proposal for a fellowship and need help doing a power analysis for how many samples I need. Basically…

Haar wavelet transform Our method transforms the raw genotype data similarly to the widely used ‘Gene- or Region-Based Aggregation Tests of Multiple Variants’ method [15] (Fig. 1). Like the Burden test, the effects of the genetic variants in a given region are summed up to construct a genetic score for…

Genomestudio2 output to use in Tassel5? 1 Hi, I got a genotyping data in Genomestudio 2. I want to export the data to use in Tassel5 for PCA, LD, and GWAS analysis. The problem is, when I load the data into Tassel5, it is put in as a numerical data,…

How to convert multiple .vcf files into single .ped (PLINK compatible files)? 0 Hi everyone, I am a newbie to the whole bioinformatics world and I need to analyse WGS data from several case samples. I have now several individual .vcf files and would like to use PLINK for Quality…

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Introduction to RNAseq I Day 3 Nicolas Rochette (EEB/ISG, UCLA) Karolina Kaczor-Urbanowicz (Oral Biology & Medicine, UCLA) UCLA Institute for Quantitative and Computational BiologyOver-representation (or enrichment) analysis is a statistical method that determines whether genes from pre-defined sets (ex: those beloging to a specific GO term or KEGG pathway) are…

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PLINK basic command line usage 0 Hey, I am new to PLINK. I run a tutorial of how to calculate polygenic risk score under a tutorial. choishingwan.github.io/PRS-Tutorial/target/#standard-gwas-qc I run the part of # Standard GWAS QC and the code is as follows: plink –bfile EUR –maf 0.01 –hwe 1e-6 –geno…

Genome assembly In this study, we de novo assembled the plum, Prunus mira, and Prunus davidiana genomes for the first time and improved the peach and apricot genomes by integrating single-molecule real-time (SMRT) long-read sequencing (PacBio), short high-quality Illumina paired-end sequencing, and Hi-C technology. First, we used SMRT reads (99−130 Gb,…

steps Collect and isolate the DNA or genome. WGS techniques generate from bacterial samples multiple short reads that can be assembled based on overlapping regions (de novo assembly), and/or mapped to a previously published reference genomes, which then enable the comparison between bacterial strains that genetically diverge at a single…

Why rvtest skipped all genes in analysis? 0 Sorry that I’m not a native English speaker, so maybe I did not make myself clear somewhere. If so, please forgive me and welcome to ask. I tried to do gene-level association analysis with Rvtests tools ( github.com/zhanxw/rvtests ). But rvtest detect…

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Previous GWAS for CM susceptibility in populations of European ancestry identified 21 risk loci. ———- Attendees should also have some basic familiarity with genomic data such as those arising from NGS experiments. Registration deadline: 15th of February 2020, > 30  days before the start date = 30% cancellation fee. **Geometric…

Tool:Genotype Imputation Workflow 0 Hello, I recently had to perform a genome-wide association study and performed genotype imputation to increase the number of SNPs I can evaluate. For that I used the Michigan Imputation Server. I combined all the necessary preprocessing steps and optional filtering steps in an easy to…

probability of two samples sharing a SNP by error 1 I’m trying to calculate the probability of the same snp occurring in two different samples by chance. I’m pretty lost here, below are the parameters I have, I’m calling SNPs at ≥1% of the reads in targeted, ultradeep sequence data….

Are there some methods can be used to do association analysis in a very small size group? 0 Sorry that I’m not native English speaker, so maybe I did not make myself clear somewhere. If so, please forgive me and welcome to ask. we foung a new trait in our…

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…

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Is there a way to find the GWAS traits to a gene programmatically? 0 Hello folks, I would like to use a gene name (e.g. DOCK2) or its ENSEMBL ID as input, and get as output the reported GWAS traits to the respective gene. I did give a look into…

DOI: 10.18129/B9.bioc.FunciSNP     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see FunciSNP. Integrating Functional Non-coding Datasets with Genetic Association Studies to Identify Candidate Regulatory SNPs Bioconductor version: 3.11 FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in…

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…

Is it recommened to filter ethenic background outlier before imputation? 0 Hi All, I was wondering if it is recommended to remove the ethenic background outlier to perform imputation using Minimac4 or imput2? For example, Should I be considering only one Ethenic group and remove all the samples from the…

How to find Standard Error (SE) values when not provided in GWAS summary stats? 2 Hi everyone! I’m trying to do a fixed effect meta-analysis on a couple of GWASes based on p-values, Standard error and effect estimates (Beta) using METAL genetics software. For one of my GWAS studies SE…

Introduction Chronic obstructive pulmonary disease (COPD) is a chronic respiratory disorder that progresses slowly and is characterized by an obstructive ventilatory pattern, which is rarely reversible. The main risk factors are active smoking, genetic factors, and air pollution. In particular, COPD has been a major public health problem and will…

PRS from a dataset on which the GWAS is based on 0 I am using the PRSice tool to calculate PRS scores for a dataset (d1) using a set of weights from the PGS catalog. Although the weights were generated from a different cohort (d2), it appears that the original…

PRS using PGS Catalog 1 When using PRSice for PRS calculation of target data using a file of variants from the PGS catalog, does the variant file from the PGS catalog replace the GWAS summary statistics (referred to as “base data” in the tutorial)? I had previously found this similar…

Resequencing of soybean accessions from low latitudes To investigate the genomic basis for the natural variation in soybean adaptation to low latitudes, we conducted whole-genome resequencing of a panel of 329 soybean accessions collected from 15 countries and covering all soybean subgroups in which 165 accessions are from in low-latitude…

custom reference panel 0 Hi all, i am embarking on creating a custom reference panel by selecting specific samples. my question is how do I select the samples? i can see that the plink distance matrix would be a good option, but otherwise, can you advise what other options are…

Genotype representation with 0, 1, 2 – what do they mean? 1 Hello all, I am currently learning about phasing and imputation, and I have come across a few ways of representing genotypes. As I understand it, 0 refers to the reference allele while 1 the alternate allele. 0/0 refers…

GWAS Power Calculation for Quantitative Trait 0 Hi All, I’m fairly new to computational genetics and I am planning on conducting a GWAS of general cognitive ability. I’m planning on using summary statistics so the data are already collected. I am struggling with post-hoc power calculations for a quantitative trait….

1001 Genome_SNP Matrix 0 Hi everyone, I am learning to do GWAS analysis in Arabidopsis. I used some accessions from the 1135 list (1001 genomes project)for a GWAS experiment. I have some questions about the genotype data. I find there are several different genomes data including .vcf format and .hdf5…

1001 Arabidopsis SNP 1 Hi everyone, I am learning to do some GWAS analysis in Arabidopsis. I used some accessions from the 1135 list (1001 genomes project)for a GWAS experiment. I have some questions for the genotype data. I find there are several different genomes data including vcf format and…

GWAS with phenotype adjusted for covariate (age, sex, PC, batch, centre) using PLINK or external linear model and take residual? 0 Hi everyone, I am conducting GWAS analysis using PLINK but I wonder should I use PLINK to adjust the phenotype for fix effect (age, sex, PC, batch, centre) or…