Tag: plink

How to genome-wide association analysis using survival analysis in Plink? 0 Hi, The most common GWAS association analyses use logistic regression. Currently, I want to do the association with survival analyses (E.g. Cox regression model) since my outcome of interest is a time-to-event variable. How can do it using Plink?…

Are package downgrades a necessary evil in Conda? 1 I am just trying to get my head around using conda environments. I created a conda environment for a project containing plink2, plink, R and bcftools. When I installed plink, using mamba install -n autozygosity -c conda-forge plink, I got the…

Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, et al. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 2007;17:1665–74. Article  CAS  PubMed  PubMed Central  Google Scholar  Chang CC, Chow CC, Tellier LC, Vattikuti S,…

Gillespie, C. F., Phifer, J., Bradley, B. & Ressler, K. J. Risk and resilience: genetic and environmental influences on development of the stress response. Depress Anxiety 26, 984–992 (2009). CAS  PubMed  PubMed Central  Article  Google Scholar  Silveira, P. P. et al. Cumulative prenatal exposure to adversity reveals associations with a…

Ai H, Fang X, Yang B, Huang Z, Chen H, Mao L et al. (2015) Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat Genet 47:217–225 CAS  PubMed  Article  Google Scholar  Alexander DH, Lange K (2011) Enhancements to the ADMIXTURE algorithm for individual ancestry estimation. BMC…

Changes in ped and map files in PLINK 1 Hello all, I want to do QC with Plink but I want to have the changes of QC in my ped and map files after QC. I used the items below but received .bim, .fam, and .bed files. My ped and…

NAME SYNOPSIS DESCRIPTION EXAMPLES BASIC OPTIONS SITE FILTERING OPTIONS INDIVIDUAL FILTERING OPTIONS GENOTYPE FILTERING OPTIONS OUTPUT OPTIONS COMPARISON OPTIONS AUTHOR NAME VCFtools v0.1.12a − Utilities for the variant call format (VCF) and binary variant call format (BCF) SYNOPSIS vcftools [ –vcf FILE | –gzvcf FILE | –bcf FILE]…

Study cohort description We used data on a total of 172,270 individuals of Japanese and East Asian ancestry. Of these, data on 165,098 individuals were obtained from BBJ, which has enrolled ≥200,000 participants to date. BBJ is a multi-institutional hospital-based genome cohort that collected participants affected with at least one…

Updating hg 18 .bim file with lifted .map and .bed file 0 Hello, I am trying to update rsids in an hg18 .bim file with an hg38.bed and hg38.map file. I’ve tried the following: system(“./plink –file plink_hg38 –make-just-bim –out newBim –allow-extra-chr”) but got the error: Error: Failed to open plink_hg38.ped….

Using a phenotype file with several phenotype columns- PLINK2 1 Hi all, I have created a tsv file ( phenotypes.tsv ) that includes phenotypes that I am using for a plink command with the –phenom flag. The first column is the #IID col with sample names that match the names…

How can I keep INFO value when convert bgen to VCF by using plink2? 1 I am working on file handling for GWAS. When I converted bgen to VCF by using plink2 with a commands below, all INFO (and also FILTER) columns became “.” in the output VCF files. A…

PRSice (pronounced ‘precise’) is a software package for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS). PRSice can run at high-resolution to provide the best-fit PRS as well as provide results calculated at broad P-value thresholds, illustrating results corresponding to either, can thin SNPs according to…

Bcftools equivalent of vcftools conversion to ped & map 1 I am converting a VCF to ped & map thus in vcftools vcftools –gzvcf ZZZZZTYT.vcf.gz –plink –out ZZZZZTYT which works fine. However, I have been searching and searching, can bcftools do the same with a bcf? bcftools • 103 views…

Significant gene-AD associations With the GWAS summary data from the IGAP and eQTL summary data from BRAINEAC, we performed both SMR and HEIDI tests to estimate the gene-AD associations in three human brain regions: frontal cortex, temporal cortex, and hippocampal regions. For the frontal cortex and hippocampal regions, we obtained…

** Bioinformatics Scientist for Whole Genome and Whole Exome Sequencing ** The NeuroGenomics and Informatics (NGI) Center lead by Dr. Carlos Cruchaga at Washington University School of Medicine is recruiting a Bioinformatics Scientist to work on Whole Genome and Whole Exome Sequencing. We are seeking an experienced, self-motivated, self-driven scientist…

Extact SNPs ID’s and their Values with IID, Additive and dominance components 0 I’m dealing with GWAS data and I have 2M records of the .bed file, I’m New to P-link, Can anyone please help me with the Plink command which can Extract all SNPs Id’s and their Values with…

Using QCTOOL v2 to process UK Biobank .bgen files – why so slow? 0 I’m currently using QCTOOL v2 to process imputed .bgen files from UK Biobank, however they seem to be processing very slowly. Is this normal? My command is pretty basic; I’m filtering out a list of SNPs…

Hi, I was trying to run regenie workflow in ukb rap (part E). github.com/dnanexus/UKB_RAP/blob/main/GWAS/regenie_workflow/partE-step2-qc-filter.sh All the previous steps ran perfectly without any error. But in this step partE-step2-qc-filter.sh I am getting dx: error: unrecognized arguments: –bfile ukb23155_c22_b0_v1 –no-pheno –keep natd_wes_200k.phe –autosome –maf 0.01 –mac 20 –geno 0.1 –hwe 1e-15 –mind…

How to Select data for a SNP for all samples using PLINK 0 Hello Folks, I’m very new to this plink. The below task has been assigned, any reference/blogs/Articles much appreciated. Q: Be able to select data for an SNP for all samples using PLINK please help plink • 49…

Fricke, R., Eschmeyer, W. N. & van der Laan, R. (eds). Eschmeyer’s Catalog of Fishes: Genera, Species, Rererences. researcharchive.calacademy.org/research/ichthyology/catalog/fishcatmain.asp. Electronic version, Accessed 15 October 2021. Nelson, J. S. Fishes of the World 4th edn, 372 (Wiley, 2006). Google Scholar  Chen, X. H., Lin, K. B. & Wang, X. W. Outbreaks…

apt-format-result, where is the –annotation-file? 0 Hi everyone! I want to create a PLINK file from the axiom analysed batches using this script: apt-format-result –calls-file <file> –annotation-file <file> –export-plinkt-file My calls-file was generated in step 7 of the APT software. However, I can’t find any annotation-file (or any *.db file)….

Merge only bim files with plink 0 Hello For the same dataset they provide a single BED and FAM files for all the chromosomes. However, the BIM files are split in chromosomes. I would like to generate the VCF file with the genotyping calls of all chromosomes but I need…

Díaz, S. et al. Summary for Policymakers of the Global Assessment Report on Biodiversity and Ecosystem Services of the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services (IPBES, 2019). Fisher, R. A. The correlation between relatives on the supposition of Mendelian inheritance. Earth Environ. Sci. Trans. R. Soc. Edinb. 52,…

Cooper, G. S., Bynum, M. L. K. & Somers, E. C. Recent insights in the epidemiology of autoimmune diseases: improved prevalence estimates and understanding of clustering of diseases. J. Autoimmun. 33, 197–207 (2009). PubMed  PubMed Central  Google Scholar  El-Gabalawy, H., Guenther, L. C. & Bernstein, C. N. Epidemiology of immune-mediated…

Hello, I used and edited the command line to use –vcf to import vcf file. I used these commands: for chr in $(seq 1 22); do      plink –vcf /dbGAP/GTEx_Analysis_2017-06-05_v8_WholeExomeSeq_979Indiv_VEP_annot.vcf.gz            –chr $chr            –recode            –out…

What software to use for GWAS with repeated longitudinal quantitative phenotype data? 0 I have quantitative data that has been collected at 4 different time points. Before treatment, 1 month after, 1 year after and 2 year after. I have generated Linear Mixed Models in R to obtain the residuals….

Hello, Thank you for developing the incredible tool that plink2 is. I have received the error “Error: No valid entries in –score file.” when using PLINK v2.00a2.3LM AVX2 Intel (24 Jan 2020). However, I don’t receive the error using the same data and arguments with a PLINK v2.00a2LM 64-bit Intel…

Control: reopen -1 Control: tags -1 confirmed Control: tags -1 upstream Control: forwarded -1 Christopher Chang <chrch…@alumni.caltech.edu> Hi Christopher (and Dylan), I verified the latest version (29 Jan 2022) of plink2 with the same result for the CI test we are doing in Debian (which was written by Dylan): $…

How to find out why PRSice-2 excludes ambiguous SNPs 0 When I use PRSice to calculate PRS，it alerts it excludes 25 SNPs from the base data. But how could I know the reason why they are ambiguous? Could I explore more why they are ambiguous? Question2: If I use PRSice…

Plink2.0 unrecognized flag: –het 1 Hi, I’m trying to run plink2.0 to calculate heterozygosity ratio, through the command: plink2.0 –pfile myFile –het but I receive this error: Error: Unrecognized flag (‘–het’) I honestly don’t have any clou about it and about it’s not recognized by plink2.0 as flag. Has this…

Plink Alternative Phenotype File Columns not being Read 0 Hi, I have a plink alternative phenotype file with the following format: FID IID Phenotype 1 2 1 1 3 0 etc. As outlined in the plink documentation. zzz.bwh.harvard.edu/plink/data.shtml#pheno However, when I run the following command : plink –bfile ../Plink_Files/plink –logistic…

Introduction Sleep is a complex neurological and physiological state. It is defined as a natural and reversible state of reduced responsiveness to external stimuli and relative inactivity, accompanied by a loss of consciousness.1 Sleep disorders can be classified as seven major categories: insomnia disorders, sleep-related breathing disorders, central disorders of…

1. Wang, J. & Jia, H. Metagenome-wide association studies: fine-mining the microbiome. Nat. Rev. Microbiol. 14, 508–522 (2016). CAS  PubMed  Google Scholar  2. Moschen, A. R. et al. Lipocalin 2 protects from inflammation and tumorigenesis associated with gut microbiota alterations. Cell Host Microbe 19, 455–469 (2016). CAS  PubMed  Google Scholar …

What file type does “PLINK –block” accept as input? 0 Hi, I have set of SNPs (distributed over all the chromosomes) and I am trying to do some haplotype block estimation to identify whether some of them are part of the same haplotype block, etc. It seems like “PLINK –blocks”…

I am a new user of PLINK and am analysing some SNP data for the first time. After creating a .bim file with $ plink –file my_data –make-bed I notice that for several SNPs my data is different from dbSNP e.g. rs145496306: BIM file: A G dbSNP: G>A,T rs3813199: BIM…

SNP extraction 0 I want to extract specific SNPs of interest i have in a text file into an additive genetics model so that each SNP can be in a 0/1/2 format for each subject using genetics info in from PLINK (.bed, .bim, and .fam files). How can i do…

I’m using the software plink2 (www.cog-genomics.org/plink/2.0/) and I’m trying to iterate over 3 variables. This software admits an input file with .ped extention file and an exclude file with .txt extention which contains a list of names to be excluded from the input file. The idea is to iterate over…

Merging genotyping array VCFs and then running kinship analysis 0 Hello, I have about 4200 array genotyping VCFs (from the Illumina Infinium CoreExome-24 Kit) and I have merged them using bcftools merge. The chip has 500K exonic SNPs. These are trio data – which means 1700 of them are probands,…

One-hot encoding for PLINK or VCF 0 I want to write an autoencoder for SNP data. Is there an established way to one-hot-encode binary PLINK or VCF input? I believe that can be done by manipulating PLINK’s bed file but am afraid to do something wrong. By one-hot encoding I…

Error: PLINK does not support more than 2^31 – 3 variants. 0 Hi there, I was converting my vcf file into bfiles in plink, and I got an error ‘Error: PLINK does not support more than 2^31 – 3 variants’. We recommend other software, such as PLINK/SEQ, for very deep…

Population-wise decay of linkage disequilibrium (LD) 0 I have three different populations, would like to plot LD with R using plink generated ld files. There is no information on multi-population LD here and so far all reported to plot single LD plot. I’ll appreciate any help R snp next-gen GBS…

What is the best way to load bgen files into python? 0 I am new to the BGEN format, (I mainly work with PLINK formatted files or VCFs). I have been trying to load a series of BGEN files to python using bgen-reader; however, there has been some issues that…

Snakemake restricted wildcard combinations 1 Hi, I’m new to snakemake and haven’t seen something like this in tutorials I’ve tried. I have a data frame with unique keys, chromosomes, start positions, and end positions. I essentially want to loop over every group to do an operation. How would I assign…

principal component analysis on pool-seq SNP data 0 I would like to perform principal component analysis on a pool-seq SNP dataset. I’ve been looking into methods for doing this, but have had trouble finding examples that may apply for pooled data as opposed to individual genotypes. For example, I’m not…

Plink to bimbam format for gemma-wrapper 0 Hi, I want to use gemma-wrapper tool which needs files in BIMBAM format. Plink can convert from plink to BIMBAM format but it is very different from the real BIMBAM format. Alleles come in two columns while BIMBAM needs them in mean genotype…

Duplicate ID in bed file 2 I am using PLINK v1.90b3s 64-bit (17 Jun 2015) to generate a LD matrix from 1000G VCF file for a long list of SNPs. I use this command to convert VCF to bed file plink –vcf ALL.chr22.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz –make-bed –out binary_fileset I then use this…

principal compoent analysis on pool-seq SNP data 0 I would like to perform principal component analysis on a pool-seq SNP dataset. I’ve been looking into methods for doing this, but have had trouble finding examples that may apply for pooled data as opposed to individual genotypes. For example, I’m not…

Source: plink2 Version: 2.00~a3-211011+dfsg-1 X-Debbugs-CC: debian…@lists.debian.org Severity: serious User: debian…@lists.debian.org Usertags: regression Dear maintainer(s), With a recent upload of plink2 the autopkgtest of plink2 fails in testing when that autopkgtest is run with the binary packages of plink2 from unstable. It passes when run with only packages from testing. In…

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…

Calculating polygenic score using plink 0 Hi I am trying to calculate PRS in test sample after getting best SNPs from PRSice 2 with highest R2 My target data is in the form of bed,bim, fam for 22 chromosomes, I want to use plink for specific p-value threshold in this…

BAM dataset to Genotype data conversion using PLINK 1 You must use a genotype caller in order to obtain genotypes from a .bam file. It’s not possible to ‘convert’ .bam to genotypes. There’s a lot of options, but maybe using bcftools is the most simple. Take a read of this…

No block substitutions in plink BIM file? 0 The BIM file from PLINK contains the variant information that accompanies a BED file. The variants called are based on exome sequencing. However, I encounter a strange issue. The BIM file consists of only single nucleotide substitutions, insertions, and deletions of base…

SHAPEIT phased haps file does not contain my SNPs of interest 0 I produced a haps file using SHAPEIT, as below. However, when I query it to look for my 12 SNPs of interest, only 3 are in there. Does anyone know why? (PS they are not in the snp.strand.exclude…

1. Wandeler, P., Hoeck, P. E. & Keller, L. F. Back to the future: Museum specimens in population genetics. Trends Ecol. Evol. 22, 634–642 (2007). PubMed  Google Scholar  2. Bi, K. et al. Unlocking the vault: Next-generation museum population genomics. Mol. Ecol. 22, 6018–6032 (2013). CAS  PubMed  PubMed Central  Google…

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…

I’d like to phase the SNPs in a vcf file and output consensus files for each haplotype, as suggested in this post: www.biostars.org/p/298635/ I’ve managed to install beagle in a conda environment: conda create -n beagle -c conda-forge -c bioconda beagle conda activate beagle When I run beagle using this…

UK Biobank Ref/Alt Allele Count PLINK2 0 Hi all, I have UK Biobank .BGEN and .Sample files, and I am trying to output sample major additive allele counts using PLINK 2 software. The PLINK 2 software manual states that REF alleles are now counted. Am I correct in assuming that…

plink –geno filters variants with good genotype rate 0 Hi there, I’m using plink v1.9. I have a list of variants that I’m interested in checking out. After filtering with –geno 0.2, some of the variants that have less than 20% of missing genotype rate are eliminated, when they should…

identification of ROH using plink 0 Hello All I generated vcf file using GATK (First Haplotypecaller –> CombinedGVCF –> GenotypeGVCF and then Hard filtering ). After this, I converted filtered vcf file into plink binary PED files (.bed, .fem, .bim, plink v1.9) using –make-bed command. However, when I used these…

Plink2 –keep Removing All Samples 1 I am trying to include the –keep and –remove options in my plink2 command. I am finding that despite my files for these options having identical text to the main file’s IDs, all the samples are removed. Command: plink2 –bfile pca_final –keep EUR.sample –remove…

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,…

Human research participants We have complied with all relevant ethical regulations and informed consent was obtained from all participants. This work was approved by the Cornell University IRB under protocol 1506005662. Animal research This work was approved by the Cornell University IACUC under protocol 2009-0044. Welfare and handling of all…

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…

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…

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…

1. Hoegh-Guldberg, O. & Bruno, J. F. The impact of climate change on the world’s marine ecosystems. Science 328, 1523–1528 (2010). CAS  PubMed  Google Scholar  2. Chou, C. et al. Increase in the range between wet and dry season precipitation. Nat. Geosci. 6, 263–267 (2013). CAS  Google Scholar  3. Li,…

VCF file generation from multiple samples fro PCA 0 I am trying to generate vcf file for 80 samples(human) and use it for pca. But when trying to get eigen vectors using plink it says genotyping rate is 0.12 and when i remove snps with missing data threshold all data…

Best tool for genotype – phenotype correlation 0 Hello, I need to perform genotype – phenotype correlation analysis. I know PLINK could be used for such purpose, but with PLINK many file preparation steps need to be done before running the actual step. I have VEP annotated VCFs. Maybe other…

Why does write.ped remove the first locus? 0 In order to get a VCF file from genind, I am going through hierfstat function write.ped() and then with plink I convert the result to vcf. This is my code (apologies, but I cannot provide a reproducible data for this particular scenario):…

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…

Population stratification with PCA 1 Hi all! I have a genotype dataset in plink format. Now I want to correct for population structure with PCA in association analysis. I split my dataset to training and testing datasets. I want to do the PCA only in the training dataset and use…

How to convert GEN or .gen format from impute.me to vcf on windows 10? 1 I tried for days to convert a gen file to vcf but it did not work. I am a beginner so i don’t know what are in vcf files and gen files or how they…

How to import dosage information to plink binary files? 0 Hi All, I recently converted a very large Topmed imputed VCF files into a plink format. The command I used to convert this VCF was plink1.9 –vcf ${VCF} –make-bed –out ${VCF}_binary. Additionally, I also spent a significant amount of time…

I have a large dataset whose autosomes I was able to successfully phase and impute using TOPMed. I have tried doing the same with the X chromosome but keep running into issues. Before trying to impute with TOPMed, I did per-individual QC and per-marker QC, then ran checkVCF, and corrected…

Plink1.9 error -chr not recognised 1 Hello, I am trying to run PLink on my tped file (SNP data set) to test for linkage disequilibrium, but it appears as if I need to set some chromosome options because I get some error at some line. My data is not mapped….

Convert plink files from 0 I have plink files where the .bim file is in the following format, and I want to convert the chr:pos column into rsIDs. 1 1:10177:A:AC 0 10177 AC A 1 1:10352:T:TA 0 10352 TA T 1 1:11008:C:G 0 11008 G C 1 1:11012:C:G 0 11012…

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…

Plink v2.0 does not produce a Z-compressed file (.zst) 0 Good morning, I would like to convert a merged VCF in a Plink compressed format (.pgen, .psam and .pvar files), so I run plink2 –vcf MyMerged.vcf.gz –make-pgen –zst-level 3 –out MySamples It basically works, as it produces such files: ls…

PLINK map format spliiting by chromosome 0 hi everyone I have a PLINK mapfile whit for columns including chromosome name, snp id, Genetic distance (morgans) (All column is zero), Base-pair position. NC1.1 rs1 0 145 NC1.1 rs2 0 201 NC2.1 rs3 0 208 . . NCn.1 rsn 0 509 I…

Recreating QC of 1000 Genomes project – removing non overlapping SNPs 0 Hi everyone, I am attempting to recreate the the quality control analysis performed in the 1000 genomes project (tcag.ca/documents/tools/omni25_qcReport.pdf). I am fairly new to performing QC on a dataset, and am currently stuck on section 5.1 of the…

PLINK dosage data – convert and/or read in R 1 I have PLINK dosage files in the form pgen/psam/pvar. I would like to know how to do either/both of the following: Convert the file set to bed/bim/fam files (hard-calls) Read the allele dosage from pgen into R as a continuous…

Can someone explain PLINK allele REF/ALT management strategy? 0 Sometimes when merging two plink files, the Reference (REF) and Alternative (ALT) alleles may be reversed, e.g. REF G ALT A versus REF A ALT G. The main reason for that is the default action of PLINK. You see, when using…

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…

Hi All, I am having a problem merging all chromosomal UK biobank files. I ran the following command. plink2 –bfile /path/to/file/ukb_imp_chr1 –pmerge-list /path/to/file/merge.list –maf 0.01 –hwe 1e-6 –make-pgen –out /path/to/file/ukb_imp_allchr I also tried plink2 –bfile /path/to/file/ukb_imp_chr1 –pmerge-list /path/to/file/merge.list –maf 0.01 –hwe 1e-6 –make-bed –out /path/to/file/ukb_imp_allchr The merge.list has the following…

UK Biobank Imputed Genotypes 0 I am using the UK Biobank Imputed Genetic data set and I was wondering if it is possible to use PLINK (or any other software) to view the actual calls for each SNP ranging in value from 0 –> 2 (including fractions)? I have been…

1. Peyrot, M. in Aspects of Globalisation: Mobility, Exchange and the Development of Multi-Cultural States 12–17 (2017). 2. Damgaard, P. et al. 137 ancient human genomes from across the Eurasian steppes. Nature 557, 369–374 (2018). CAS  PubMed  Article  ADS  PubMed Central  Google Scholar  3. Hemphill, B. E. & Mallory, J….

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,…

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…

Distance matrix PCA 0 Hi all, I generated PCA values for the 1000genomes dataset using PLINK. I know how to plot the values for PC1 and PC2, but my question is how can I generate a distance matrix to select near samples based on populations? Like for example if I…

Hello, I need to use SHAPEIT for phasing only since I will conduct CH (compound heterozygous) analysis for recessive rare variant.. I will not perform imputation.  I am running SHAPEIT, and I see in the log file it says: Parameters :  * Seed : 1442251531  * Parallelisation: 12 threads  *…

New datasets for ancestry estimation and imputation? 0 What datasets are people using nowadays for genotype imputation and ancestry estimation? HapMap and 1000 Genomes are good, but it was some years since their release and both have some limitations on the number of populations included and resolution (especially HapMap which…

Beagle 5 error: No VCF records found in the specified interval 0 Hi, I am running into an issue while doing Imputation with Beagle 5 and not sure what is causing the error. I have vcf files converted from PLINK by the following command ./plink –bfile qcd_in–chr 20 –recode vcf-iid…

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)…

❯ plink1.9 –homozyg –help PLINK v1.90b6.22 64-bit (3 Nov 2020) www.cog-genomics.org/plink/1.9/ (C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3 –help present, ignoring other flags. –homozyg [{group | group-verbose}] [‘consensus-match’] [‘extend’] [‘subtract-1-from-lengths’] –homozyg-snp <min var count> –homozyg-kb <min length> –homozyg-density <max inverse density (kb/var)> –homozyg-gap <max internal gap…

Sample ID ERROR in converting dosage file (.txt) to VCF in PLINK 2.0 0 Hi, I have a dosage file (.txt format; alternative allele count 0-2) that I would like to convert to a VCF through PLINK 2.0 but am running into sample ID issues. I am attempting the following…

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…

Forum:Can we merge two VCF files – a RNAseq VCF and a Whole genome Sequencing (WGS) VCF to do PCA? 0 I’m quite new to this variant calling and analysis area. We have around 30 samples of RNAseq data of tumor and normal samples. I performed variant calling and obtained…

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…