Statistical population genomics, methods in molecular biology, vol. In this tutorial, we will use plink to analyse some real and some example largescale snp data, to giv e a demonstration of what the program can do e. Sep 29, 2019 haploview tutorial pdf haploview software demo. This would cause three score reports to be generated. A toolset for working with human genetic variation data. A pdf version of this website is available for download. This is generally harmlessthere is no a priori reason to prefer one tiebreak scheme to the other. Data is typically in the form of case control data with ascertainment bias. This page describes specialized plink input and output file formats which are identifiable by. Introduction to the plink software plink overview i summary statistics for quality control i allele, genotypes frequencies, hwe tests i missing genotype rates i inbreeding, ibs and ibd statistics for individuals and pairs of individuals i nonmendelian transmission in family data i sex checks based on x chromosome snps i tests of nonrandom genotyping failure. First, if plink andor plink2 are not installed on your system, download and unzip the appropriate binaries v1. Polygenic risk score tutorial sarah medland quantitative genetics, qimr berghofer 16072014. Cancer genetics, for identifying problematic mutations.
Plink is a free, opensource whole genome association analysis toolset, designed to perform a range of basic, largescale analyses in a computationally efficient manner the focus of plink is purely on analysis of genotypephenotype data, so there is no support for steps prior to this e. Using plink for genomewide association studies gwas and. Data management and summary statistics with plink springerlink. By way of introducing some of the features and approaches of plinkseq, this page provides a tutorial that uses pseq and the r interface to plinkseq to work with nextgeneration sequence data from the genomes project. Run a gwas on a dataset for an slerelated disease in dogs by using plink. Understand the genetics of important human diseases.
With simulated data, i need to construct polygenic score and the. The plink documentation has a nice discussion of what is included in these. The software is designed flexibly to perform a wide range of basic, largescale genetic analyses. A tutorial on conducting genomewide association studies. Introduction to plink tutorial national bioinformatics courses february 2014 1. Even though some of the steps discussed in this article could be performed in conventional statistical packages such as r, a software package specifically dedicated to the. Steps involved preparing the files required to run plink profile. The nature of the test statistic will be mentioned in the log and printed to the console.
Studies gwas genomewide association handson tutorial to. Thecurrentdirectory is a central notion for plink usage, because by default, plink will load. Quality control and statistical analysis article pdf available february 2018 with 1,975 reads how we measure reads. Statistical analysis of genomewide association gwas data jim stankovich menzies research institute. Merlin format, mach, plink, plink2, and best practices of snp imputation i have been fighting with the different gwas file formats recently, and getting confused more and. The first parameter should be the name of a file with range.
The following plink commands will allow you to reformat your input. Pdf a tutorial on conducting genomewide association. It is not meant to replicate all the workflows you might use in a complete analysis, but instead touch on a sampling of the more typical scenarios you may come across in your own studies. Often, the path of the current directory willbedisplayedbeforetheprompt,asinfigure2. Rplinkseq is implemented as an extension library, which enables access to the plinkseq. Specifically, it must be normalized such that allele1 column 5 in the bim file is the reference allele on the plus strand and allele2 is the alternative allele on the plus strand. Part of the methods in molecular biology book series mimb, volume 2090. Plink has a variety of output files depending on the analysis. This tutorial aims to provide a guideline for conducting genetic. We re not going to run these because they take a lot of time, instead we re just going to copy the files with the cp command below. Rplinkseq is an r package that allows access to plinkseq projects directly from r, so that rs rich set of statistical and visualisation tools can be utilised. For example, to get rid of all first degree relations parentchild and siblingsibling, you could run. Even though the content has been prepared keeping in mind.
Plink is a free, opensource whole genome association analysis toolset, designed to perform a range of basic, largescale analyses in a computationally efficient manner. Statistical analysis of genomewide association gwas data. They all have a common aimto demonstrate the utility and draw attention of the r environment for statistical genetics or. A tutorial on conducting genomea wide association studies. Aug 05, 2019 haploview tutorial pdf haploview software demo. Genomewide association study analysis using genabel. Plink gplink haploview institute for behavioral genetics. As alpha and beta testing continue, plink2 will become increasingly usable on its own, but for now its better to think of it as a supplement to rather than a replacement for v1. Introduction to r on rpackages power of r r is modular there is a core and you can load packages containing custom functions. Aug 14, 2019 haploview tutorial pdf haploview software demo.
You may want to create your own plink files to calculate ld or do other things with the data. To reduce the data size of the example data in plinkqc. Plink tutorial amended from two tutorials that the plink author shaun purcell wrote, see and teaching materials and example dataset at download plink from in this tutorial, we will use plink to analyse some real and some example largescale snp data, to give a demonstration of what the program can do e. The input file should be in plink bed format and have undergone qc similar to that in the gwas qc module to ensure only high quality observed genotypes are included and that they have been resolved to the reference sequence. We will use two datasets of snp genotype calls from the pilot 3 exon study. Plink is used in terminal dos mode in ms windows environment. The focus of plink is purely on analysis of genotypephenotype data, so there is no support for steps prior to this e. Plink is a versatile program which supports data management, quality control, and common. Introduction to the plink software transferrin data. The second file should contain a variant id and the key quantity on each nonempty line except possibly the. Using plink to analyse these data this tutorial is intended to introduce some of plink s features rather than provide exhaustive coverage of them. Plink is a free, commonly used, opensource wholegenome association analysis toolset designed by shaun purcell.
The nhgriebi gwas catalog, a curated resource of snptrait associations duration. Topic plink, simplified and adapted to use gplink a graphical version of. Mar 28, 2020 european journal of human genetics, epub. Plink and qc and practical verneri anttila these presentations were filmed during the september 20 statistical genetics workshop, part of the broade workshop series. The pruned dataset was generated with the following two plink commands. Gwas with plink i run a gwas analysis of transferrin with plink. In this tutorial, we will walk through using plink to work with the data. The pseq command line tool is the primary interface of the plinkseq library. Alternatively, if you know that you will only ever run plink on files in a single folder, then you can paste plink. This should produce a list of the help topics that are available.
The specific focus is to provide a platform for analytic tool development for variation data from largescale resequencing and genotyping projects, particularly wholeexome and wholegenome studies. Some of the central design features of plink seq include. Within this chapter we introduce the basic plink functions for reading in data, applying quality control, and running association analyses. A tool set for wholegenome association and population. Plink currently supports following functionalities. A tutorial on conducting genomewide association studies bio3. This tutorial is prepared for the students and researchers at the undergraduategraduate level who wish to get good solutions for optimization problems fast enough which cannot be solved using the traditional algorithmic approaches. European bioinformatics institute emblebi 1,848 views. Welcome to the snp genomewide association tutorial. I make sure to apply some quality controls i command to apply qc thresholds such as maf 0. Specifically, it must be normalized such that allele1 column 5 in the bim file is the reference allele on the plus.
Polygenic risk score tutorial qimr berghofer medical. Using filters to include all individuals and snps mind individual missing rate geno genotype missing rate maf snp allele frequency plink bfile example mind 1 geno 1 maf 0 maxmaf 0 filter maxmaf sets the maximum minor allele frequency command must still be entered all on a single line plink tutorial, october. The package adegenet 1 for the r software 2 implements representation of. However, it is also possible to complete all tutorials using plink 1. I am using the score command in plink to estimate profiles for individuals based on an allelic. Studies gwas genomewide association handson tutorial. Plink has the ability to output files for beagle and can recode a.
Skip the automatic webbased version check stdout or s. Plink is a versatile program which supports data management, quality control, and. In this introduction to plinkseq, we will use one toy vcf dataset and pseq, pbrowse and the r interface to view, filter and summarise these data. Pdf a tutorial on conducting genomewide association studies. First ensure that pseq is properly installed on your system, by typing the following at the command prompt pseq help. As such, aspects of the code, database format, range of.
This is a comprehensive update to shaun purcells plink commandline. We suggest that after downloading plink you first try the tutorial. A tool set for wholegenome association and populationbased linkage analyses article in the american journal of human genetics 8. Futhermore, it is not intended as an analysis plan for whole genome data, or to represent anything close to best practice.
They all have a common aimto demonstrate the utility and draw attention of the r environment for statistical genetics or genetic epidemiology. Also, it is almost 300 pages long, so please consider this before printing. How to create plink files for genome project phase 3. Mar 12, 2019 haploview tutorial pdf haploview software demo. A tutorial on how to do genomewide association studies gwas in plink. Understand the genetics of other important traits, e. Additionally, plink is designed to work in conjunction with r, and can output files to be processed by certain r packages. The sexes must also be specified in the plink fam file without any missing values as these are required for proper. This means that all the core features of the plinkseq library i. This page provides links to the currently available releases of the plinkseq library and associated resources. Revision has been made in the context of genomewide association studies gwass. The sample is definitely female 2 x chromosomes by intensities. The following tutorial is designed to systematically introduce you to a number of techniques for genomewide association studies. Native text genotype file format for oxford statistical genetics tools, such as impute2 and.
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