Tag: beagle

It’s the holiday season, and what’s better to do than cuddle up in bed and watch a movie? We want to make sure you’re not missing out on some binge-worthy biotech movies this December. So, we have created a watchlist just for you. Here are some biotech movie recommendations to…

Wang, A. L. & Wang, C. C. Viruses of the protozoa. Annu. Rev. Microbiol. 45, 251–263 (1991). Article  CAS  PubMed  Google Scholar  Banik, G., Stark, D., Rashid, H. & Ellis, J. Recent advances in molecular biology of parasitic viruses. Infect. Disord. – Drug Targets 14, 155–167 (2015). Article  Google Scholar …

BAM file for phasing 0 Hi all, I’m new in bioinformatics, and i’m trying to do phasing and imputation to WGS-level. For imputation with Beagle, I would like to make a bref file from a vcf file. And I have to phase the reference panel for that. Is a BAM…

ANGSD beagle generation returning empty file 0 Hello Biostars community, I am struggling quite a bit with ANGSD these days as it seems that no code I provide to the machine is working as intended. I want now to produce a beagle file but the following script is returning me…

The pioneering cartographer of the human genome, Craig Venter, discusses synthetic biology and his new book, “Sorcerer II: The Expedition That Unlocked The Secrets of The Ocean’s Biome” with Noema Editor-in-Chief Nathan Gardels. Nathan Gardels: Generative AI has been heralded lately as one of the great game-changing innovations of our…

I’ve recently updated to macOS Sonoma and started using {renv} when using cmdstanr started causing fatal errors and crashing RStudio (i.e., loading it using library(cmdstanr) or just making function calls using cmdstanr::). After lots of trial and error, it appears to be an RStudio thing since I can run the…

De Rubeis S, He X, Goldberg AP, Poultney CS, Samocha K, Cicek AE, et al. Synaptic, transcriptional and chromatin genes disrupted in autism. Nature. 2014;515:209–15. Article  PubMed  PubMed Central  Google Scholar  Iossifov I, O’Roak BJ, Sanders SJ, Ronemus M, Krumm N, Levy D, et al. The contribution of de novo…

Error Information: Description of issue –I recently updated my Macbook (M2, 2022) to Sonoma and can’t get RStudio to start now. Attempted steps taken to fix –I have tried to reinstall Quartz, R, and RStudio without success. R will open on its own, but not RStudio. System Information: RStudio Edition:…

Encuesta Nacional de Salud 2000 Since 1988, Mexico has established periodical National Health Surveys (Encuesta Nacional de Salud (ENSA), originally conceived as National Nutrition Surveys) for surveillance of Mexican population-based nutrition and health metrics. In this study, we use data and samples collected from the survey carried out in 2000,…

I am trying to install RStudio on my M1 Mac (2020) with Sonoma. However I run into the following problem.\ R version – ➜ ~ R –versionR version 4.3.1 (2023-06-16) — “Beagle Scouts”Copyright (C) 2023 The R Foundation for Statistical ComputingPlatform: aarch64-apple-darwin20 (64-bit) RStudio – Version 2023.06.2+561 (2023.06.2+561) R Session…

I’m working with a resequenced genome of a non-reference species. The VCF contains ~7 mln of SNPs, all with their relative position on their own chromosome. I have a 10.01 % of missing data, so I need to impute these NA. I eventually settled for Beagle v5 as a tool,…

Why Beagle v5.4 fails during phasing large genotypic data set? 0 I am trying to phase large genotypic data set (~330 samples and ~25 millions SNPs) by using Beagle v5.4. My command is this: java -Xmx160g -jar ./beagle.22Jul22.46e.jar gt=./lines_ch1.vcf.gz ref=./ref_lines.bref3 chrom=1 map=./genmap_ch1.map nthreads=60 window=10.0 out=./pased_lines_ch1 impute=false The job ends when…

Sample collection Previously, we collected nasal samples from WTD in northeastern Ohio focusing on metropolitan area parks11. In the present study, we expanded geographical study area by approximately 1000-fold to target the entire state of Ohio. We collected 1522 nasal swabs from WTD across 83 of Ohio’s 88 counties from…

conform-gt error “Duplicate marker” 0 I am using below scripts: java -jar conform-gt.24May16.cee.jar ref=Chr01.merged_files_Miss_new.vcf.gz gt=batch1-8_450k_edited.beagle.39474SNPs_new.vcf.gz chrom=1 match=ID out=mod.chr01.consistent to align my input file to the reference (unphased yet). Below is the error message: Below is the error message: Exception in thread “main” java.lang.IllegalArgumentException: Duplicate marker Chr01.merged_files_Miss_new.vcf.gz]: 1 1 1_1.9e+07 C…

I have been attempting to install a package that requires cmake. However, Rstudio can’t seem to find it for some reason: R version 4.3.1 (2023-06-16) — “Beagle Scouts” Copyright (C) 2023 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin22.4.0 (64-bit) R is free software and comes with ABSOLUTELY NO WARRANTY….

Four years ago, a few hundred miles off the coast of West Africa, a crane lifted a bulbous yellow submarine from the research vessel Poseidon and lowered it into the Atlantic. Inside the sub, Karen Osborn, a zoologist at the Smithsonian Institution who was swaddled in warm clothes, tried to…

For a few months I have been encountering an issue on multiple different computers and across different versions of R where none of the interactive windows from the utils package and base R are displaying correctly. The functions where this occurs is choose.files, askYesNo, and file.choose (first 2 from the…

System details RStudio Edition : Desktop RStudio Version : RStudio 2023.06.01 “Mountain Hydrangea” 547dcf86, 2023-07-06) for macOS OS Version : Ventura 13.4.1 – macOS – Apple Macbook Pro 13-inch M1, 2020 R Version : 4.3.1 (2023-06-16) — “Beagle Scouts”, Platform: x86_64-apple-darwin20 (64-bit) Steps to reproduce the problem I just downloaded…

Phenotype data We obtained yield datasets for rice (Oryza sativa L.) from 207,331 trials with 8524 cultivars during the 38 years from 1980 to 2017. The data were obtained from field trials at 110 public agricultural experimental stations in Japan conducted by the Institute of Crop Science of the National…

Dark, P. & Gent, H. Pests and diseases of prehistoric crops: a yield ‘honeymoon’ for early grain crops in Europe? Oxford J. Archaeol. 20, 59–78 (2001). Article  Google Scholar  Mira, A., Pushker, R. & Rodriguez-Valera, F. The Neolithic revolution of bacterial genomes. Trends Microbiol. 14, 200–206 (2006). Article  CAS  PubMed …

Beagle log not matching SNP data 0 Hello, I am trying to impute the genotypes of 32 individuals to WGS with Beagle 5.4 and I found inconsistences between beagle logs and my SNP data. I run Beagle with this: java -Xss51m -Xmx64g -jar beagle.22Jul22.46e.jar gt=genotype_Chr1.vcf ref=training_ref_Chr1.vcf.gz out=genotypeChr1_imputed These are the…

Overview of the integrative mapping approach to generate a dog reference epigenome. (A) Diagram of 11 primary tissue types from beagle dogs sampled for the study. (B) Synopsis of next-generation sequencing (NGS) methods, data integration approaches, and analyses performed for the integrative profiling the dog epigenome. See also Methods. (C)…

Tools for SNP imputation 0 Hello, I am working with polyploid plant species (tetraploid, hexaploid, octaploid). I have genotype by sequencing (GBS) SNP data from different sequencing platforms like Affymetrix and SeqSNP. Now, I want to perform SNP imputation for some species and increase the number of SNPs and also…

99, 12451260 (2016). Genet. eCollection 2023. 36, 29362937 (2020). Genet. These assays include massively parallel regulatory assays134, which test synthetic regulatory sequences by screening variants in thousands of untranscribed or untranslated sequences for functional effects in a single experiment, and CRISPR techniques that allow for the introduction of mutations into…

In this study, for the first time, we presented an overview of the ROH patterns of the Kazakh national dog breed Tazy from a genome-wide perspective. According to the obtained results, there was strong evidence of distant inbreeding in this breed about 50 generations ago, as most ROH fell into…

Ethics statement This study relied on analyses of genetic data from the UKB cohort, which was collected with informed consent obtained from all participants. Data for this study were obtained under the UKB applications licence number 66995. All data used in this research are publicly available to registered researchers through…

published on 2023-06-26T14:18:56Z r download 11 DOWNLOAD shoxet.com/2ur4D2 This shortcut allows you to download from YouTube with the choice of quality and also you can download from Facebook photos and video with the ability to choose the quality and also you can download from Twitter with the choice of quality…

Hi everyone, I am trying to run the Beagle 5.4 software where it needs to read a VCF file. The error message I have is: Exception in thread “main” java.lang.IllegalArgumentException: VCF record format error: 1 131079320 BHD0100437271 G A . PASS . GT at vcf.VcfRecGTParser.ninthTabPos(VcfRecGTParser.java:87) at vcf.VcfHeader.isDiploid(VcfHeader.java:73) at vcf.RefIt.<init>(RefIt.java:130) at…

Ethical compliance This project was approved by the Wellcome Sanger Institute Animal Welfare and Ethical Review Body and complied with all relevant ethical regulations regarding animal research and human studies. Human cells were obtained from HipSci24, where they were collected from volunteers recruited from the National Institute for Health and…

How to extract only neutral markers from low-coverage whole genome sequencing? 0 I was wondering how to extract only the neutral markers from low-coverage whole genome sequencing either from a VCF file or a Beagle file. Any idea on how to do this? Should this be done by calculating the…

Forum:What Are The Most Common Stupid Mistakes In Bioinformatics? 78 While I of course never have stupid mistakes…ahem…I have many “friends” who: forget to check both strands generate random genomic sites without avoiding masked (NNN) gaps confuse genome freezes and even species but I’m sure there are some other very…

Topic participation The examine protocol was accredited by the ethics committees of Osaka College and associated medical establishments in addition to the Translational Well being Science and Know-how Institute (Faridabad). Japanese people (n = 343) for whom intestine metagenome shotgun sequencing had been carried out in earlier research had been included on…

Subject participation The study protocol was approved by the ethics committees of Osaka University and related medical institutions as well as the Translational Health Science and Technology Institute (Faridabad). Japanese individuals (n = 343) for whom gut metagenome shotgun sequencing were performed in previous studies were included in this study46,47,48. Among these…

runs of homozygosity 0 I am finding runs of homozygosity,. Step by step moving i have found RoHs first then i made plink bfiles updated ids then recoded vcfs then phased chromosome-wise and merged into one and now i have again changed it into the beagle format using vcf2beagle software…

ARG-Needle and ASMC-clust algorithms We introduce two algorithms to construct the ARG of a set of samples, called ARG-Needle and ASMC-clust. Both approaches leverage output from the ASMC algorithm11, which takes as input a pair of genotyping array or sequencing samples and outputs a posterior distribution of the TMRCA across…

I updated my Rstudio to the following It was fine.But now, it keeps crashing. I don’t do anything unusual. It keeps crashing after there is some simple errors with the code (when library is not loaded etc.). Or just randomly while staying idle for a few minutes. Now, I cannot…

The International Human Genome Sequencing Consortium announces the completion of a “working draft” … [+] human genome sequence. Craig Venter (left, Celera Genomics), President Bill Clinton (center), and Francis Collins (right, NHGRI) at the White House Press Conference regarding the completion of the working draft of the human genome. NIH…

Biological introductions are unintended “natural experiments” that provide unique insights into evolutionary processes. Invasive phytophagous insects are of particular interest to evolutionary biologists studying adaptation, as introductions often require rapid adaptation to novel host plants. However, adaptive potential of invasive populations may be limited by reduced genetic diversity—a problem known…

Why is Beagle v5.4 (imputation) not giving Allele Frequencies (AF) and DR2 in my output? 0 Hi there! I have just imputed some low-coverage (<4x) whole genome sequencing samples using a WGS reference panel (>10x) and Beagle v5.4: java -jar beagle.22Jul22.46e.jar gt=${file} impute=true gp=true ne=100 nthreads=16 ref=${refvcf} out=${outfile} However, the…

I wish to calculate the kinship matrix from a batch of Next Generation Sequencing (NGS) data. Previously, I have tried to use PCAngsd 0.98 to output the matrix, but it seems that this option does not exist any more since the previous version of the software PCAngsdv2. www.popgen.dk/software/index.php/PCAngsd www.popgen.dk/software/index.php/PCAngsdv2 Would…

How to get BEAGLE files from VCF with angsd? 0 Hello, I want to output genotype likelihood BEAGLE file from VCF file with angsd, in order to use them in pcangsd later. But with the following command I obtain an error message. angsd \ -GL 2 \ -out output_file \…

I had a vcf file with imputed genotypes from beagle like this: ##fileformat=VCFv4.2 ##filedate=20210504 ##source=”beagle.18May20.d20.jar” ##INFO=<ID=AF,Number=A,Type=Float,Description=”Estimated ALT Allele Frequencies”> ##INFO=<ID=DR2,Number=1,Type=Float,Description=”Dosage R-Squared: estimated squared correlation between estimated REF dose [P(RA) + 2*P(RR)] and true REF dose”> ##INFO=<ID=IMP,Number=0,Type=Flag,Description=”Imputed marker”> ##FORMAT=<ID=GT,Number=1,Type=String,Description=”Genotype”> ##FORMAT=<ID=DS,Number=A,Type=Float,Description=”estimated ALT dose [P(RA) + 2*P(AA)]”> ##FORMAT=<ID=GP,Number=G,Type=Float,Description=”Estimated Genotype Probability”> #CHROM POS ID…

Hello, I have tried running mrbayes-v3.2.6 on my university cluster with a text block in my nexus file, as below: begin mrbayes; set autoclose=yes nowarn=yes; CHARSET mtgenome = 1-16701; partition favored = 1: mtgenome; set partition = favored; unlink shape=(all) pinvar=(all) statefreq=(all) revmat=(all) tratio=(all); prset applyto=(all) ratepr=variable; lset applyto=(1) nst=2…

Samples RNA-seq We used the same publicly available data source of human post-mortem brain samples as Van Booven et al.7, which were collected from the New South Wales Brain Tissue Resource Center. Van Booven et al.7 also performed differential splicing, but they used different methods, included individuals from disparate ancestral…

PharmAust says it’s Phase-2 trial for the treatment of canine B-cell Lymphoma with Monepantel (MPL) is expected to be completed by mid-2023. So far, the company has had some solid results demonstrating anti-cancer activity, with one patient surpassing 240 days with stable disease and an excellent Quality of Life (QoL)….

From VCF to BEAGLE format with multiple chromosomes 0 I wish to convert a VCF file in the BEAGLE format with all chromosomes contained in the VCF file with vcftools. Unfortunately, it seems there is no option to use vcftools with all the chromosome, at least one chromosome has to…

convert beagle genotypes to vcf 0 Hi, I have a phased beagle file which I generated through Angsd v0.935. I would like to use the beagle utility program beagle2vcf.jar. However I keep getting this error: java -jar beagle2vcf.jar rs markers bgl_comb ? > vcf Exception in thread “main” java.lang.IllegalArgumentException: Alleles…

Sample collection We obtained the short read sequences for 33 brown bear genomes, four polar bears (Ursus maritimus) and two American black bears (Ursus americanus), publicly available from NCBI’s SRA repository (Table S1 and Fig. 1a)12,13,15,16,40,51,65. Next, we selected from our private collections a total of 95 additional samples for sequencing, among…

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]…

Charles Darwin’s voyage on HMS Beagle led to a treasure trove of observations: the behaviour of cuttlefish, a parasitic ichneumon wasp feasting inside live caterpillars, fossils of extinct giant sloths and ‘mastodons’. The result, of course, was his theory of natural selection. Darwin needed the complex natural world to inspire…

ERROR: Variant physical position must be monotonically increasing 0 I want to calculate XPEHH for each SNP position. When I run the following command selscan –xpehh –vcf B10_beagle.vcf –vcf-ref D6_beagle.vcf –map MAP.map –threads 8 –out B10vsD6 I get this error ERROR: Variant physical position must be monotonically increasing Ch2:66 66…

pcangsd 0 when I use PCAngsd software，Processing beagle format files obtained from ANGSD，I want to output the file in NPY format，but there is an error：value error：ndarray is not C-contiguous，and I do not konw how to modify my command for pcangsd，can anyone help me ？ PCAngsd • 16 views Login before…

Extreme environments present profound physiological stress. The adaptation of closely related species to these environments is likely to invoke congruent genetic responses resulting in similar physiological and/or morphological adaptations, a process termed “parallel evolution” (1). Existing evidence shows that parallel evolution is more common at the phenotypic level than at…

BEAST and BEAGLE installed using conda environment, how to connect? 1 Hello experts, I have 2 version of BEAST, the BEAST v 1.10 is installed through conda environment, where BEAST v 2.6 have the binary file. Further I have installed BEAGLE v 5.1 using conda environment as I’m unable to…

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…

phasing VCF files with missing genotype 0 I want to phasing a VCF file with missing value(./.), the output I want get (a VCF also)is all the genotype are phased, but the ./. will not be imputed. I have tried shapeit and beagle, but both of them impute the missing…

Phasing with Beagle 5.2 and no reference panel 0 Hi everyone, I have a question about phasing with Beagle 5.2 without a reference panel. I have seen in answers in a couple other posts about Beagle that trying to phase with too few samples and no reference panel is not…

Hardy-Weinberg Equilibrium and MAF filtering post imputation 0 Hi, I have 5 million variants after imputation using Beagle 5.2 after filering low confidence imputation ( DR2 < 0.9). Pre-imputation QC was that I removed rare variants MAF < 0.05 and use only variants with no missing genotype data (–geno 0…

Using a phased reference assembly to phase sample genotypes 0 I’ve been trying without success to phase the variants of about 30 samples in a 5Mb non-recombining region. I have a phased genome assembly of the region but so far I have not been successful in using that to inform…

Forum:map file for BEAGLE imputation 0 Hello Community, I am having an issue with BEAGLE V5.2 throwing an error stating all my loci have the same genetic position when they most certainly do not. I have posted the error and a sample of the top of the map file I…

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…

Sequencing of Shorea leprosula genome Sample collection Leaf samples of S. leprosula were obtained from a reproductively mature (diameter at breast height, 50 cm) diploid tree B1_19 (DNA ID 214) grown in the Dipterocarp Arboretum, Forest Research Institute Malaysia (FRIM). DNA extraction Genomic DNA was extracted from leaf samples using the…

1. Thomson, M. R. A. Geological and palaeoenvironmental history of the Scotia Sea region as a basis for biological interpretation. Deep Sea Res. II 51, 1467–1487 (2004). Article  ADS  Google Scholar  2. Maldonado, A. et al. A model of oceanic development by ridge jumping: Opening of the Scotia Sea. Glob….

You can use this script in two ways read tons of millions of P values from stdin # python zcat pval.txt.gz | qqplot.py -out test -title “QQ plot on the fly” # julia zcat pval.txt.gz | qqplot.jl –out test –title “QQ plot on the fly” warning : If you have…

You can use make a QQ plot in the following ways. one-liner for reading tons of millions of P values from the pipe # python zcat pval.txt.gz | qqplot.py -out test -title “QQ plot on the fly” # julia (recommand to run it in the REPL) zcat pval.txt.gz | qqplot.jl…

You can use this script in two ways read tons of millions of P values from stdin # python zcat pval.txt.gz | qqplot.py -out test -title “QQ plot on the fly” # julia zcat pval.txt.gz | qqplot.jl –out test –title “QQ plot on the fly” warning : If you…

Hi, I have been trying to get a dosage file from vcf, map and fam files. For that, I have written this bash script : plink –fam plink.fam –map plink.map –dosage one.vcf –write-dosage However, I got this error: –dosage: Reading from one.vcf. Error: Line 1 of one.vcf has fewer tokens…

Hey everyone, I’m having some trouble with the imputation step in my GBS pipeline. I’m following the FastGBS pipeline basically as written up until this point. Before running Beagle, i’ve performed a filtering step using vcftools (though I get the same error whether or not I do this; I just…

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….

Beagle 5.2 for imputation, outofmemory or ‘bus error’ any help? 0 Hi, I was trying to use beagle 5.2 for imputation of genotype data (N=62k). I was using chr21 with chunks of 3MB (total 12 chunks running in parallel). This tool is very fast. The problem is every time I…

phase_trio.sh | searchcode PageRenderTime 24ms CodeModel.GetById 16ms app.highlight 5ms RepoModel.GetById 1ms app.codeStats 0ms /Phase/phase_trio.sh github.com/BioinformaticsArchive/fCNV Shell |…

Beagple 5.2 phasing error 0 Hi everyone, I’m trying to phase a multi-sample (12 samples) vcf file with the first chromosome. I got this vcf after pruning with plink and recode it back to vcf. The file looks like this: 1 112 . C T . . PR GT ./….

Error when Phasing with Beagle 5.2 0 I’m having trouble phasing a multi-sample (9-samples) vcf file produced by gatk HaplotypeCaller with Beagle 5.2. I do not have a genetic map or reference panel. I am working with a very heterozygous group of organisms (sea urchins). When I run beagle with…

  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…