Tag: beagle

As of July 2015, the VCFtools project has been moved to github! Please visit the new website here: vcftools.github.io/man_0112a.html

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]…

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Molecular biologists: let’s reconnect with nature

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…

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Variant physical position must be monotonically increasing

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…

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pcangsd

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…

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Parallel genomic responses to historical climate change and high elevation in East Asian songbirds

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…

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BEAST and BEAGLE installed using conda environment, how to connect?

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…

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Phasing using Beagle with a map file

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…

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phasing VCF files with missing genotype

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…

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Phasing with Beagle 5.2 and no reference panel

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…

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Hardy-Weinberg Equilibrium and MAF filtering post imputation

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…

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Using a phased reference assembly to phase sample genotypes

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…

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map file for BEAGLE imputation

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…

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No VCF records found in the specified interval

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…

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The genome of Shorea leprosula (Dipterocarpaceae) highlights the ecological relevance of drought in aseasonal tropical rainforests

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…

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Cenozoic climatic changes drive evolution and dispersal of coastal benthic foraminifera in the Southern Ocean

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….

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Cool Bioinformatics Scripts With Python

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…

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GitHub – Zilong-Li/BioScripts: Cool Bioinformatics Scripts

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…

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Cool Bioinformatics Scripts | PythonRepo

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…

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I can’t get a dossage file using PLINK

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…

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Beagle 5.2 Imputation Issue, understanding output

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…

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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….

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Beagle 5.2 for imputation, outofmemory or ‘bus error’ any help?

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…

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phase_trio.sh | searchcode

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 |…

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Beagple 5.2 phasing error

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 ./….

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Error when Phasing with Beagle 5.2

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…

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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…

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