Category: GWAS

Labelling SNPs in a stacked manhattan plot with karyoploteR

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…

Continue Reading Labelling SNPs in a stacked manhattan plot with karyoploteR

How do I merge imputed GWAS data

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…

Continue Reading How do I merge imputed GWAS data

Bioinformatics Data Engineer – Chennai

About Job CTC Undisclosed Job Location Chennai Experience 0 – 3 yrs Description Its a dynamic and results-oriented environment to work in but thats why we like it. There are countless opportunities to learn and grow, whether thats exploring new technologies in hackathons, or redefining the roles and work of…

Continue Reading Bioinformatics Data Engineer – Chennai

Workshop proceedings: GWAS summary statistics standards and sharing: Cell Genomics

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…

Continue Reading Workshop proceedings: GWAS summary statistics standards and sharing: Cell Genomics

Bioinformatics QA | Santa Clara, CA

Bioinformatics QA | Santa Clara, CA | Persistent Systems, Inc. Location: Start New Search: bioinformatics scientistamerican securitynext generation sequencingcomputational biologyassay developmentngsrochepython rgenomicsbioinformaticsbiostatisticsoriginsmolecular biologydnablueprintmachine learningvisualizationphysicshivphd Persistent Systems, Inc.Santa Clara, CA Full-time Experience in Next Generation Sequencing (NGS) Seeking a talented and tech-savvy Bioinformatics QA to join our North American security practice…

Continue Reading Bioinformatics QA | Santa Clara, CA

Revision DNA sequencing and genotyping – 300820 – Genes, Genomics And

GGHH 300820 2021 Workshop: DNA and RNA sequencing and Genotyping Why do we need to sequence the human genome? Why do we need to sequence genomes from different populations? DNA Sequencing Targeted DNA sequencing (Sanger Sequencing): sequencing small targeted regions of the genome to tests for the presence/absence of mutations…

Continue Reading Revision DNA sequencing and genotyping – 300820 – Genes, Genomics And

Statistical Geneticist – Cancer job with Paramount Recruitment

Statistical Geneticist – Cancer *Based in Oxford but flexible working options* This is a fantastic opportunity to join a rapidly growing biotechnology company who specialise in the development of innovative technologies, products and offerings for the benefit of cancer patients. They are looking for a skilled Statistical Geneticist to join…

Continue Reading Statistical Geneticist – Cancer job with Paramount Recruitment

SNP-based heritability in GWAS (GREML)

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…

Continue Reading SNP-based heritability in GWAS (GREML)

Calculate z-scores from GWAS summary stats

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…

Continue Reading Calculate z-scores from GWAS summary stats

Error: Could not open temporary file.

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…

Continue Reading Error: Could not open temporary file.

Calculating PRS in UK Biobank

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…

Continue Reading Calculating PRS in UK Biobank

Research Logistician in Bioinformatics – Academic Positions

Reference : SF30548Internal and external offer until 8th of November 2021 For the “Louvain Institute of Biomolecular Science and Technology” (LIBST), of the Sciences and Technology Sector (SST)  Main working place :  Louvain-la-Neuve Full-time and permanent contractStarting date : as soon as possible   UCLouvain is the largest university of…

Continue Reading Research Logistician in Bioinformatics – Academic Positions

How to do a power analysis for samples needed for a GWAS? : bioinformatics

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…

Continue Reading How to do a power analysis for samples needed for a GWAS? : bioinformatics

Wavelet Screening: a novel approach to analyzing GWAS data | BMC Bioinformatics

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…

Continue Reading Wavelet Screening: a novel approach to analyzing GWAS data | BMC Bioinformatics

Genomestudio2 output to use in Tassel5?

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,…

Continue Reading Genomestudio2 output to use in Tassel5?

How to convert multiple .vcf files into single .ped (PLINK compatible files)?

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…

Continue Reading How to convert multiple .vcf files into single .ped (PLINK compatible files)?

Associate Director, Human Genetics and Bioinformatics at Alector

At Alector, our mission is to develop therapies that empower the immune system to cure neurodegeneration. Our team is solely focused on developing cures for some of the most challenging diseases facing our society. We are supported in this mission by experienced and accomplished scientists and board members, leading healthcare…

Continue Reading Associate Director, Human Genetics and Bioinformatics at Alector

Biocmanager Install Vs Install Packages

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…

Continue Reading Biocmanager Install Vs Install Packages

3-year fully funded Phd position in plant-microbe interaction, GWAS and bioinformatics

Agricultural sustainability can be achieved through the reduction of fertilizers. When exposed to nutrient limitations, such as phosphate starvation, plants are able to recruit specific microbes. This ability strongly relies on the plant genome which shows great variation among varieties even of the same species. With the final aim of…

Continue Reading 3-year fully funded Phd position in plant-microbe interaction, GWAS and bioinformatics

Bioinformatics Biomedical Scientist – Bilsborough Lab

Bioinformatics Biomedical Scientist – Bilsborough Lab – Inflammatory Bowel Diseases Drug Discovery and Development Apply Now Share Requisition # HRC0697538 Join us in accelerating the pace of research and discovery within our unique IBD3 lab! Cedars-Sinai provides virtually every known gastroenterologic analytical procedure and treatment…

Continue Reading Bioinformatics Biomedical Scientist – Bilsborough Lab

PLINK basic command line usage

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…

Continue Reading PLINK basic command line usage

Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach

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,…

Continue Reading Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach

whole genome sequencing method

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…

Continue Reading whole genome sequencing method

Why rvtest skipped all genes in analysis?

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…

Continue Reading Why rvtest skipped all genes in analysis?

genomic data scientist jobs

Provide strategic planning and perform analysis or simulations independently or in a . 401(k) savings plan match.…, Requires a Ph.D. in Biochemistry, Biotechnology, Molecular/Cell Biology, Plant Biology, or a related field and 0-3 years of relevant postdoctoral or industrial……, In addition, the analyst will help advance the groups collective expertise…

Continue Reading genomic data scientist jobs

Bioinformatics Research Scientist

Bioinformatics Research Scientist – 93904 Organization: JG-Joint Genome Institute Lawrence Berkeley National Lab’s (LBNL, www.lbl.gov/) Joint Genome Institute Division (jgi.doe.gov/) has an opening for a Bioinformatics Research Scientist to join the team. In this exciting role, you will develop new computational methods to investigate gene regulation and regulatory sequence properties…

Continue Reading Bioinformatics Research Scientist

american educational research journal abbreviation

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…

Continue Reading american educational research journal abbreviation

Genotype Imputation Workflow

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…

Continue Reading Genotype Imputation Workflow

probability of two samples sharing a SNP by error

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….

Continue Reading probability of two samples sharing a SNP by error

Are there some methods can be used to do association analysis in a very small size group?

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…

Continue Reading Are there some methods can be used to do association analysis in a very small size group?

P-values far too high for quantitative regenie phenotype

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…

Continue Reading P-values far too high for quantitative regenie phenotype

Amgen Is Recruiting A Principal Scientist

Employer Amgen Location South San Francisco, CA Posted Sep 20, 2021 Ref R-121973 Discipline Science/R&D, Biology, Biotechnology Hotbed  Biotech Bay, Ideal Employer Required Education Bachelors Degree Position Type Full time Amgen is a leading global biotechnology company, with a mission to serve patients around the world. The Clinical Biomarkers &…

Continue Reading Amgen Is Recruiting A Principal Scientist

Is there a way to find the GWAS traits to a gene programmatically?

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…

Continue Reading Is there a way to find the GWAS traits to a gene programmatically?

Bioconductor – FunciSNP

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…

Continue Reading Bioconductor – FunciSNP

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?

Is it recommened to filter ethenic background outlier before imputation?

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…

Continue Reading Is it recommened to filter ethenic background outlier before imputation?

How to find Standard Error (SE) values when not provided in GWAS summary stats?

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…

Continue Reading How to find Standard Error (SE) values when not provided in GWAS summary stats?

SNP of the SREK1 gene is associated with COPD in Kashi

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…

Continue Reading SNP of the SREK1 gene is associated with COPD in Kashi

PRS from a dataset on which the GWAS is based on

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…

Continue Reading PRS from a dataset on which the GWAS is based on

PRS using PGS Catalog

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…

Continue Reading PRS using PGS Catalog

Genetic basis and adaptation trajectory of soybean from its temperate origin to tropics

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…

Continue Reading Genetic basis and adaptation trajectory of soybean from its temperate origin to tropics

custom reference panel

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…

Continue Reading custom reference panel

Genotype representation with 0, 1, 2

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…

Continue Reading Genotype representation with 0, 1, 2

GWAS Power Calculation for Quantitative Trait

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….

Continue Reading GWAS Power Calculation for Quantitative Trait

1001 Genome_SNP Matrix

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…

Continue Reading 1001 Genome_SNP Matrix

1001 Arabidopsis SNP

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…

Continue Reading 1001 Arabidopsis SNP

GWAS with phenotype adjusted for covariate (age, sex, PC, batch, centre) using PLINK or external linear model and take residual?

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…

Continue Reading GWAS with phenotype adjusted for covariate (age, sex, PC, batch, centre) using PLINK or external linear model and take residual?

validation of probable SNPs

validation of probable SNPs 0 Hi all, I recently got some significant SNPs from my GWAS analysis, many of these SNPs are imputed (I filtered Rsq>0.8 ). We are yet to do replication study for our findings, waiting for replication cohort samples and it might take a while for this….

Continue Reading validation of probable SNPs

What is the best QC to do on imputed UK Biobank data?

What is the best QC to do on imputed UK Biobank data? 0 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 QC’d for missingness per individual and per SNP, sex discrepancy, MAF filter…

Continue Reading What is the best QC to do on imputed UK Biobank data?

How to estimate polygenic risk score (PRSs) using the scoring files from PGSCatalog for one individual?

How to estimate polygenic risk score (PRSs) using the scoring files from PGSCatalog for one individual? 2 Hi all, I have an annotated vcf file for one individual which I want to estimate his polygenic risk score (PRS) for a certain trait, using the scoring files from the PGSCatalog. The…

Continue Reading How to estimate polygenic risk score (PRSs) using the scoring files from PGSCatalog for one individual?

How does PLINK work?

How does PLINK work? 0 Hi, I would like to know how a logistic regression in a GWAS works in detail. I have an example dataset, with SampleIDs, Genotypes (GT) in dosage formt and binary phenotypes. Now, how would the logistic regression be performed if I only want to work…

Continue Reading How does PLINK work?

How to get all genes and their annotations within a LD block?

How to get all genes and their annotations within a LD block? 0 Hi all, Thank you for your help. I identified several significant SNPs with GWAS in wheat. Next, I want to get all the genes form the haploblock where the SNPs reside. Using Emsembl, I was able to…

Continue Reading How to get all genes and their annotations within a LD block?

Oklahoma Medical Research Foundation hiring Data Analyst / Bioinformatics Specialist – OK02135701 in Oklahoma City, Oklahoma, United States

This job was posted by okjobmatch.com : For more information, please see: okjobmatch.com/ada/r/jobs/2135701 r rData Analyst / Bioinformatics Specialist r rOverview rOMRF is an independent, not-for-profit biomedical research institute adjacent to the University of Oklahoma Health Sciences Center (OUHSC) campus in Oklahoma City. Oklahoma City offers a dynamic and flourishing…

Continue Reading Oklahoma Medical Research Foundation hiring Data Analyst / Bioinformatics Specialist – OK02135701 in Oklahoma City, Oklahoma, United States

A Closer Look at Type 1 Diabetes Causal Variants

By Allison Proffitt September 7, 2021 | Stephen Rich’s group at the University of Virginia along with John Todd’s team at the University of Oxford, have been tracing the genes responsible for type 1 diabetes for years. In 2009 the team conducted the largest GWAS metanalysis of type 1 diabetes,…

Continue Reading A Closer Look at Type 1 Diabetes Causal Variants

Bioinformatics Scientist in Frederick, MD

Job DescriptionBioinformatics ScientistFull Time Direct Hire Remote positionAre you looking for bioinformatics work? Are you interested in joining a team of talented bioinformaticians dedicated to understanding the genetics of cancer? In this role you will:* Function as a scientific thought leader within for all aspects of GWAS and population genetics….

Continue Reading Bioinformatics Scientist in Frederick, MD

The Biostar Herald for Friday, September 03, 2021

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from zx8754, Istvan Albert, and was edited by…

Continue Reading The Biostar Herald for Friday, September 03, 2021

GWAS results: base pair annotation

GWAS results: base pair annotation 1 Hello, I have a question regarding annotation of GWAS results. Here is the sample files File1 Below is the File1 with HG38id column name that contains chromosome number and base pair position. HG38id 13:21325916 5:128327887 19:44906745 1:88820990 17:44981703 File2 Below is the File2 with…

Continue Reading GWAS results: base pair annotation

Dealing with P value inflation of SNPs identified by qqplot

Dealing with P value inflation of SNPs identified by qqplot 0 I’m attempting to call SNPs that changed in allele frequency in a population. The population was sequenced at two times (before and after a drought) using pooled-sequencing of the whole genome. Fisher exact tests identified 7 million SNPs, which…

Continue Reading Dealing with P value inflation of SNPs identified by qqplot

New Techniques and Complex Models

CRISPR systems that rely on inactivated Cas enzymes—that is, dead Cas (dCas) enzymes—never looked more alive. They harness the targeting power associated with CRISPR—but not the double-strand cuts. As such, they give researchers new ways to interrogate and manipulate gene function. Possibilities include CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa)…

Continue Reading New Techniques and Complex Models

normality assumption for GWAS QT

normality assumption for GWAS QT 0 Hi Planning to perform GWAS on quantitative trait using linear reg in plink. From my basic knowledge of statistics, i know that the assumption of normality (residuals) should be only approximately true. But i have seen so many papers on GWAS transforming the data…

Continue Reading normality assumption for GWAS QT

Association test to get p values and OR in plink2, and file input format

Association test to get p values and OR in plink2, and file input format 0 Are there any commands for association testing in plink2 which will output p-value and OR in the resulting output file? If so, what kind of file input do I need to use for such commands…a…

Continue Reading Association test to get p values and OR in plink2, and file input format

UK BioBank

UK BioBank 0 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 one provided by UK Biobank) where I can unsderstand the schema better? Thanks ukb UK-Biobank GWAS • 53 views Login before adding…

Continue Reading UK BioBank

Performing population stratification based on GWA tutorial

Performing population stratification based on GWA tutorial 0 Hi, I’m performing QC steps of Andries T. Marees GWA tutorial, currently I’m stuck at 7th step where you should begin the population stratification downloading a 61GB vcf.gz file of 1000genomes containing genetic data of 629 individuals from different ethnic backgrounds. Successively…

Continue Reading Performing population stratification based on GWA tutorial

GWASpower calculation

GWASpower calculation 0 Dear All, Sorry , sounds like a stupid question but been struggling with this for a while. I am trying to do post-hoc power calculation for my GWAS using GWASpower software for quantitative trait (i know many don’t prefer post-hoc power calculation, but reviewer asked me despite…

Continue Reading GWASpower calculation

Association test to get p values and OR in plink2, and file input format?

Association test to get p values and OR in plink2, and file input format? 0 Are there any commands for association testing in plink2 which will output p-value and OR in the resulting output file? If so, what kind of file input do I need to use for such commands?…

Continue Reading Association test to get p values and OR in plink2, and file input format?

Bioconductor – cageminer (development version)

DOI: 10.18129/B9.bioc.cageminer     This is the development version of cageminer; to use it, please install the devel version of Bioconductor. Candidate Gene Miner Bioconductor version: Development (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…

Continue Reading Bioconductor – cageminer (development version)

Filter duplicate ID from PLINK file

Filter duplicate ID from PLINK file 0 Hi All, I am new to SNP-chip data analysis. I have been exploring some SNP-chip data using plink 1.9, while checking the Relatedness using KING, I am getting an error of duplicate ID. I was wondering if there is any method I can…

Continue Reading Filter duplicate ID from PLINK file

Bioconductor – GGtools

DOI: 10.18129/B9.bioc.GGtools     This package is for version 3.12 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see GGtools. software and data for analyses in genetics of gene expression Bioconductor version: 3.12 software and data for analyses in genetics of gene…

Continue Reading Bioconductor – GGtools

genomic inflation factor (lambda)=1

genomic inflation factor (lambda)=1 0 Dear Community members, Does genomic inflation (lambda)= 1 indicate that there is no obvious population stratification in GWAS? I did GWAS (binary phenotype) and while running –glm in plink2, the output gives lambda=1. Even when i don’t include my principal components the lambda value is…

Continue Reading genomic inflation factor (lambda)=1

Logistic regression for GWAS analysis

Logistic regression for GWAS analysis 0 Hi, I would like to know how a logistic regression in a GWAS works in detail. I have an example dataset, with SampleIDs, Genotypes (GT) in dosage formt and binary phenotypes. Now, how would the logistic regression be performed if I only want to…

Continue Reading Logistic regression for GWAS analysis

Oklahoma Medical Research Foundation hiring Data Analyst / Bioinformatics Specialist in Oklahoma City, Oklahoma, United States

OMRF is an independent, not-for-profit biomedical research institute adjacent to the University of Oklahoma Health Sciences Center (OUHSC) campus in Oklahoma City. Oklahoma City offers a dynamic and flourishing downtown area, with a low cost of living, short commute times and a diversified economy. OMRF supports a comprehensive postdoctoral training…

Continue Reading Oklahoma Medical Research Foundation hiring Data Analyst / Bioinformatics Specialist in Oklahoma City, Oklahoma, United States

FASTQ VS VCF

Bioinformatics: What is the difference between fasta . … GWAS: Fastq to BAM to VCFFrom fastq to vcf Note: Some commands continue on the next line. Source link

Continue Reading FASTQ VS VCF

Bioinformatics Software Engineer, Cancer Genomics Research Laboratory (req2036) job with Frederick National Laboratory

PROGRAM DESCRIPTION We are seeking an enthusiastic, creative, and collaborative bioinformatics software engineer to support pipeline development and analysis for our broad portfolio of genomic studies. If you have experience designing and deploying robust, reproducible, production-quality pipelines, then come join our talented team of bioinformaticians dedicated to understanding the genetics…

Continue Reading Bioinformatics Software Engineer, Cancer Genomics Research Laboratory (req2036) job with Frederick National Laboratory

How to fix phenotype information when converting from VCF to PLINK

How to fix phenotype information when converting from VCF to PLINK 0 I have a series of VCF files (one for each chromosome) that have an incorrect values for the phenotype (all samples have the value “-9”). I have read on other questions that the make-pheno or pheno flags can…

Continue Reading How to fix phenotype information when converting from VCF to PLINK

proportion of variance

Khatami – I have addressed this at length, elsewhere. Please see: GWAS: low explained heritability There are a variety of phrases that are used; variance explained is one of them – don’t be thrown off … the concept is very simple. For example, let’s say I am trying to predict…

Continue Reading proportion of variance

linkage disequilibrium and haplotype analysis of GWAS .

  linkage disequilibrium and haplotype analysis of GWAS . 0   Hi all, I have GWAS data. I have my data in 22 chromosome files in plink format. I have imputed genotype with Sanger imputation server. I use plink for my analysis but because plink 1.9 no more supports –hap…

Continue Reading linkage disequilibrium and haplotype analysis of GWAS .