Tag: snp

Active Motif Incorporated Announces the Acquisition of Amaryllis Nucleics and their proprietary RNASeq workflow

CARLSBAD, Calif., Jan. 27, 2022 /PRNewswire/ — Active Motif Incorporated, a company with the vision of bringing epigenetics more deeply into precision medicine, announced that it has purchased Amaryllis Nucleics, a Bay Area-based start-up company focused on proprietary RNA Sequencing methods. Amaryllis Nucleics provides Active Motif with a streamlined, low-cost…

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DNA Labs International Launches the Newest Technology for Forensic Genetic Genealogy

MiSeq FGx platform by Verogen DEERFIELD BEACH, Fla. (PRWEB) January 26, 2022 DNA Labs International, which specializes in forensic DNA analysis including forensic genetic genealogy (FGG) for law enforcement agencies, government forensic labs, and attorneys, is announcing the release of their newest technology, Single Nucleotide Polymorphism (SNP) testing with…

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To use rflp analysis to detect a snp. the snp must _______.

To use RFLP analysis to detect a single nucleotide polymorphism (i.e., a SNP), the SNP must _______. To use RFLP analysis to detect a single nucleotide polymorphism (i.e., a SNP), the SNP must _______. cause disease occur in homozygous form occur within a restriction enzyme recognition sequence be present in…

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Download full list of SNPs and their coordinates in hg38

Download full list of SNPs and their coordinates in hg38 3 What is the best / standard place to get a full list of SNPs and their coordinates in hg38? I downloaded the SNPsnap database, but just realized that those coordinates are in hg19. I’m trying to figure out how…

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An intronic transposon insertion associates with a trans-species color polymorphism in Midas cichlid fishes

Conflicting results suggest a missing variant In order to narrow down candidates for the causal genetic variant, we performed genome-wide association mapping separately in individual lake populations (previously, association mapping was only performed across the whole species flock5). Interestingly, despite clear association peaks in the crater lakes (Fig. 1a, b), the…

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The Genetic Architecture of Sleep Health Scores in the UK

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…

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High-throughput analysis of ANRIL circRNA isoforms in human pancreatic islets

Abstract The antisense non-coding RNA in the INK locus (ANRIL) is a hotspot for genetic variants associated with cardiometabolic disease. We recently found increased ANRIL abundance in human pancreatic islets from donors with certain Type II Diabetes (T2D) risk-SNPs, including a T2D risk-SNP located within ANRIL exon 2 associated with…

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Do we need to apply the same p-value threshold on all 22 chromsomes?

Polygenic Risk Score Calculation: Do we need to apply the same p-value threshold on all 22 chromsomes? 1 Hi there, I am using PRSice-2 to calculate the polygenic risk score for 22 chromosomes one by one. To my understanding, since the 22 chromosomes are independent of each other, and our…

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Toll-like receptor 2/4 in Chinese patients with sepsis

Introduction Sepsis is a life-threatening organ dysfunction that results from an exaggerated host immune response to disseminate infection.1 Despite improvements in treatment strategies, sepsis remains a leading cause of death in critically ill patients worldwide.2 Low platelet number, known as thrombocytopenia, is common in infectious diseases (also sometimes referred to…

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bedtools intersect error: Invalid record in file

Hello to all I am trying to run bedtools intersect with vcf file and a bed file (my goal is to add the depth data to my VCF) I get an error running this command: bedtools intersect -a depth.bed -b fish.vcf -wa -wb > $out The error: “Error: Invalid record…

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What is SNP array testing?

What is SNP array testing? The SNP array test looks for changes in specific areas of a person’s chromosomes, such as gains (duplications) or losses (deletions). These gains or losses result in extra or missing copies of genetic material. How does SNP array work? SNP array is a type of…

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Associate Scientist, Bioinformatics – jobRxiv

Are you interested in being a key member of a bioinformatics team in a shared resource at a major cancer center?  This Associate Scientist position will support a wide array of bioinformatics research services in the Sylvester Comprehensive Cancer Center (SCCC) Biostatistics and Bioinformatics Shared Resource (BBSR) at the University…

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SNP associated contigs

SNP associated contigs 0 I am using usegalaxy.org for SNP analysis. After mapping with bowtie2 I got BAM file including QNAME FLAG RNAME POS and on variant calling I got Chrom Pos ID Ref Alt. Showing Variant position on reference genome. I want to get those sequences associated to SNP….

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Bioinformatics, Computer Science, Biology – Transcriptomic, Genomic Assays (f/m/d) – Evotec International GmbH – Biologie & Life Sciences

Evotec is a life science company with a unique business model focused on delivering highly effective new therapeutics to the patients. The Company leverages its multimodality platform, the “Data-driven R&D Autobahn to Cures”, for proprietary projects and within a network of partners including Pharma, Biotech, academics, and other healthcare stakeholders….

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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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Cytogenomic Molecular Inversion Probe Array FFPE Tissue – Products of Conception

Cytogenetic Test Request Form Recommended (ARUP form #43098) Ordering Recommendation Recommendations when to order or not order the test. May include related or preferred tests. Use to detect copy number alterations and loss of heterozygosity in FFPE specimens from products of conception. Mnemonic Unique test identifier. CMAPFFPE Methodology Process(es) used…

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Bioconductor – ProteoDisco

DOI: 10.18129/B9.bioc.ProteoDisco     Generation of customized protein variant databases from genomic variants, splice-junctions and manual sequences Bioconductor version: Release (3.14) ProteoDisco is an R package to facilitate proteogenomics studies. It houses functions to create customized (mutant) protein databases based on user-submitted genomic variants, splice-junctions, fusion genes and manual transcript…

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17q12-21 risk-variants influence cord blood immune regulation and multitrigger-wheeze

Background: Childhood wheeze represents a first symptom of asthma. Early identification of children at risk for wheeze related to 17q12-21 variants and their underlying immunological mechanisms remain unknown. We aimed to assess the influence of 17q12-21 variants and mRNA-expression at birth on development of wheeze. Methods: Children were classified as…

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Very important pharmacogene variants in the Blang population

Introduction The use of drugs should be different among diverse ethnic groups because of differences in ethnicity, age, sex, environmental factors and genetic factors. If these differences are ignored, then drug sensitivity, metabolic rate, and adverse reactions are affected, which influences the curative effect of drugs and aggravates the illness…

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How can I make sure certain SNPs are not removed during the clumping stage of PRS calculation using PRSice

How can I make sure certain SNPs are not removed during the clumping stage of PRS calculation using PRSice 1 This is a two part question. First, when implementing PRSice, is there a way to make sure certain SNPs are retained for the PRS calculation? I basically want to avoid…

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Bioconductor Tools for Microarray Data Analysis

References ………………………………………………………………………………………..478 17.1 INTRODUCTION 17.1.1 WHAT IS BIOCONDUCTOR? Bioconductor [1] is an open source software project for the R statistical computing language. The main aim of the project is to provide R packages to facilitate the analysis of DNA microarray, sequencing, SNP and other genomic data. In addition for data,…

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Reference panel data to be used for GCTA-COJO

Reference panel data to be used for GCTA-COJO 0 I performed a genome-wide meta-analysis based on summary statistics from the four cohorts to identify significant loci. Next, I would like to perform a conditional analysis using GCTA-COJO to search for SNPs independent of significant lead SNPs. I know that GCTA…

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Blast command line pipeline not working

Blast command line pipeline not working 0 Hello, I am running now a local blast pipeline using MacOs. The goal here is to take interval of the 5 best hits and then extract the SNP variants from multiple vcf.gz files. But I am facing an error which I cannot solve….

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Padding out a GVCF file with 1000G exomes to get gatk VariantRecalibrator working with a small sample

I’ve got sequencing data for a small 500 bp amplicon from a few samples. GATK best principles suggest running VariantRecalibrator on the GVCF files I generate. I’m trying to get this working, but I get an error about “Found annotations with zero variances”. Reading the gatk manual and other posts…

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Natera launches Prospera with quantification to improve kidney graft rejection testing

Natera has announced the launch of Prospera with quantification, the only cell-free DNA (cfDNA) test for kidney rejection that provides three values—the quantity of donor-derived cfDNA (dd-cfDNA), fraction of dd-cfDNA, and total cfDNA—on every report. Combining these three metrics has been shown to improve sensitivity when evaluating transplant rejection, compared…

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Mitochondrial DNA-like sequences in the human nuclear genome: Characterization and implications in the evolution of mitochondrial DNA

The complete mitochondrial genome of Flustrellidra hispida (Bryozoa, Ctenostomata, Flustrellidridae) was sequenced using a transposon-mediated approach. All but one of the 36 genes were identified (trnS2). The genome is 13,026 bp long, being one of the smallest metazoan mitochondrial genomes sequenced to date with a unique gene order when compared to…

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PLINK sanity check – Bioinformatics Stack Exchange

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…

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Large-scale genome-wide study reveals climate adaptive variability in a cosmopolitan pest

Genomic data The foundational resource for this study was a dataset of 40,107,925 nuclear SNPs sequenced from a worldwide sample of 532 DBM individuals collected in 114 different sites based on our previous project15. DNA was extracted from each of the 532 individuals using DNeasy Blood and Tissue Kit (Qiagen,…

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SNP extraction

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…

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gatk VariantRecalibrator positional argument error

I’m trying to use recalibrate my vcf using gatk VariantRecalibrator, but keep getting an error “Illegal argument value: Positional arguments were provided”. But I don’t know what this means, or how to correct it! Here’s my call: gatk VariantRecalibrator -R “/Volumes/Seagate Expansion Drive/refs/hg38/gatk download/Homo_sapiens_assembly38.fasta” -V “$OUT”/results/variants/”$SN”.norm.vcf.gz -AS –resource hapmap,known=false,training=true,truth=true,prior=15.0: “/Volumes/Seagate…

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No quality in non-variant sites GATK

No quality in non-variant sites GATK 1 Heys, I am doing the SNP calling with Haplotypecaller BP_Resolution, CombineGVCFs with convert-to-base-pair-resolution and GenotypeGVCFs with include-non-variant-sites with GATK and when I get my vcf file, the non-variant sites does not have any quality at all: #CHROM POS ID REF ALT QUAL FILTER…

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Removing contamination with SNP tools

Removing contamination with SNP tools 0 Hello everyone, Currently, I’m working on a ChIPseq dataset where I will analyze chromatin marks on transposons and genes in a fungus. Unfortunately, I got some contamination in my data from a closely related species. Because they are so similar, removing contamination based on…

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New bioinformatics tool spots hybrid fish that threaten survival of natural tilapia populations in aquaculture

A new genomics marker tool has been shown to accurately identify tilapia species and tell apart their hybrids, providing a novel resource to help develop aquaculture and empower conservation in Tanzania, Africa. Crucially, the new tool offers a cheaper solution than full genome data analysis — the current approach to…

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What is the single nucleotide polymorphism database ( dbsnp )?

The Single Nucleotide Polymorphism Database (dbSNP) is a free public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information (NCBI) in collaboration with the National Human Genome Research Institute (NHGRI). Furthermore, are there any databases for single nucleotide polymorphisms?As there…

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SNP2TFBS

SNP2TFBS Viewing variants that affect TF binding – Results – SNP identifier Chrom id (Feb 2009 GRCh37/hg19) SNP position NB. of TF factors rs1800629   dbSNP NC_000006.11 (chr6) 31543031 1 TF name  PWM score on Ref PWM score on Alt Score difference Low Score Thr High Score Thr MZF1_1-4  1024  ….

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Ethnic Diversity of DPD activity and the DPYD Gene

Plain Language Summary Fluoropyrimidine (FP; 5-FU, capecitabine) is a common chemotherapy used to treat many different cancers, including cancer of the colon and rectum, upper digestive tract, breast and head and neck. Cancer patients who receive FP chemotherapy are at risk of developing severe side effects from their treatment. A…

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the spacer of sgrna will hybridize with this sequence of dna from the fragment shown below?

James Guys, does anyone know the answer? get the spacer of sgrna will hybridize with this sequence of dna from the fragment shown below? from EN Bilgi. Solved The spacer of sgRNA will hybridize with this sequence Answer to Solved The spacer of sgRNA will hybridize with this sequence Do…

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Common and rare variant association analyses in amyotrophic lateral sclerosis identify 15 risk loci with distinct genetic architectures and neuron-specific biology

Department of Neurology, UMC Utrecht Brain Center, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands Wouter van Rheenen, Rick A. A. van der Spek, Mark K. Bakker, Joke J. F. A. van Vugt, Paul J. Hop, Ramona A. J. Zwamborn, Annelot M. Dekker, Klara Gawor, Henk-Jan Westeneng, Gijs H. P. Tazelaar, Kristel R. van Eijk, Maarten Kooyman, Ewout J. N. Groen, Michael…

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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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One-hot encoding for PLINK or VCF

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…

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Convert SNP IDs as chr:pos:effect allele:ref allele to rsIDs

Convert SNP IDs as chr:pos:effect allele:ref allele to rsIDs 0 I have a set of 58000 SNPs for which the SNP ID is in the format of: chr:pos:effect allele:ref allele (Grch37 build), but I need to convert this to rsID where one is available for the SNP. I’ve tried using…

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vcf to bgen conversion using qctool v2 yields 0 snps

Hi all, I have a vcf file that was extracted from UKB data using qctool (v2.0.6-Ubuntu16.04-x86_64) and contains data in the GP format. This contains a bunch of SNPs from a single chromosome. ❱ wc -l chromosome1.vcf 260 chromosome1.vcf Then I try to convert this file to .bgen again using…

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Dissemination of Mycobacterium abscessus via global transmission networks

Dataset construction, cluster identification and definition of DCCs Whole genome sequencing of two collections of isolates from Manchester, UK, and the Netherlands was carried out as previously described2. Briefly, DNA was extracted from colony sweeps of subcultured samples before to paired-end sequencing using the Illumina HiSeq platform. These samples were…

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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…

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Filter criteria for variants based on GBS data

Filter criteria for variants based on GBS data 0 Are there recommended filter criteria for variants based on GBS data? I currently use this filter formula that is used in bcbio for WGS based variants soft-filtering bcftools –soft-filter GATKCutoffSNP -e TYPE=”snp” && (MQRankSum < -12.5 || ReadPosRankSum < -8.0 ||…

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merge bfiles with different allele format by plink

merge bfiles with different allele format by plink 0 Hello, I want to merge two bfiles using plink. However, one bfile is written as below. 1 rs123 0 123 A G 1 rs234 0 234 G T The other file is as below. 1 rs123 0 123 1 2 1…

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GRRDUser Manual [PDF] | Documents Community Sharing

* The preview only display some random pages of manuals. You can download full content via the form below. Microsoft Word Add-In for the GenePattern Reproducible Research Document July 2009 Introduction…………………………………………………………………………………………………………………. 3 About GenePattern…………………………………………………………………………………………………… 3 How GenePattern and the GRRD Add-In Work Together…………………………………………………4 Reproducibility of Document Interactions………………………………………………………………………4 Installing and Uninstalling…

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23andme file format

23andme file format 2 What (if any) is the official file format name that 23andme uses. I’ve only seen it referred to as 23andme format. Are they complying with a more general format? If so, what is it? If not, why did they invent a new format? 23andme vcf variant…

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Genome-wide analysis reveals associations between climate and regional patterns of adaptive divergence and dispersal in American pikas

Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19:1655–1664 CAS  PubMed  PubMed Central  Article  Google Scholar  Alexander DH, Shringarpure SS, Novembre J, Lange K (2015) Admixture 1.3 software manual. UCLA Hum Genet Softw Distrib, Los Angeles Google Scholar  Angert AL, Bontrager…

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Bioconductor – VanillaICE

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see VanillaICE. A Hidden Markov Model for high throughput genotyping arrays Bioconductor version: 3.4 Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays. Author: Robert Scharpf <rscharpf at jhu.edu>, Kevin Scharpf,…

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Question about ROH analysis by Plink 1.9

Hi all, I have recently tried to estimate runs of homozygosity (ROH) from my vcf file by using plink 1.9. I ran following code to generate binary files that plink required: plink –vcf myfile.vcf –make-bed –out out_name –no-sex –no-parents –no-fid –no-pheno –allow-extra-chr This vcf file only contains one individual and…

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Obtaining The Snp Rs Number With The Chromosomal Position

Obtaining The Snp Rs Number With The Chromosomal Position 3 This question is similar to this one (Get rs number based on position). I have a text file with SNPs in the chr:position format 10:71086 10:72876 10:75794 I was wondering if there is an R package (or perhaps one in…

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snpEff: annottation problem

snpEff: annottation problem 0 Hi everyone. I am using snpEff on my personal computer, and when I try to annotate a VCF file I get this error: [[0Kjava.lang.OutOfMemoryError: Java heap space[[0KM at java.util.Arrays.copyOfRange(Unknown Source)[[0KM at java.lang.String.<init>(Unknown Source)[[0KM at java.lang.StringBuilder.toString(Unknown Source)[[0KM at java.io.BufferedReader.readLine(Unknown Source)[[0KM at java.io.BufferedReader.readLine(Unknown Source)[[0KM at org.snpeff.fileIterator.LineFileIterator.readNext(LineFileIterator.java:46)[[0KM [[0K at…

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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…

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Why some SNP’s are not assigned to any gene?

Why some SNP’s are not assigned to any gene? 0 Hi everyone, I am doing polygenic risk analysis (PRS) ; As you may know PRS is done based on SNP’s. On the other hand, I would like to do some visualizations at gene level. Thus, I used rsnps library (ncbi_snp_query…

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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…

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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…

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The sardine run in southeastern Africa is a mass migration into an ecological trap

INTRODUCTION Large-scale annual migrations occur in an extraordinary range of animals, from insects to the great whales. While the driving mechanisms of these migrations are varied and sometimes poorly understood, they often represent a way of optimizing conditions for breeding and adult fitness when these are in conflict. Often, populations…

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Rockefeller Disability Jobs – Director of Research Bioinformatics in New York, New York, United States

Job: IRC26893 Description Job Title Director of Research Bioinformatics Laboratory / Department Hospital Department Description The Rockefeller University Hospital is funded by the National Institutes of Health and has 20 patient beds for clinical research. The Hospital provides researchers with an opportunity to conduct clinical studies, and offers both normal…

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Parabon Recreates Egyptian Mummy Faces From Ancient DNA

New Snapshot methods for low-coverage sequencing bring hidden data to life Scientific Poster Image Scientific Poster Image Scientific Poster Image RESTON, Va., Sept. 15, 2021 (GLOBE NEWSWIRE) — At the 32nd International Symposium on Human Identification (ISHI), being held this week in Orlando, Florida, Parabon NanoLabs will unveil for the…

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SNP exon region UCSC

SNP exon region UCSC 2 how i can get SNP in only exons regions genome with UCSC? UCSC get the all SNP of gene region, and there is no filter option to get only exon region. tx ucsc SNP exon • 245 views • link updated 2 hours ago by…

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snpEFF not able to download GRCH38 ?

snpEFF not able to download GRCH38 ? 2 HI Why snpEff not able to download GRCH38 ? Always its showing error, But its work well with GRCH37 reference. Thanks for your comments. likithreddy@Curium:~/Downloads/snpEff_latest_core/snpEff$ java -jar snpEff.jar download GRCh38.76 java.lang.RuntimeException: Property: ‘GRCh38.76.genome’ not found at org.snpeff.interval.Genome.<init>(Genome.java:106) at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681) at org.snpeff.snpEffect.Config.readConfig(Config.java:649) at…

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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…

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Rvtests SKAT-O output

Rvtests SKAT-O output 0 Hi there, After running SKAT-O, the output has some columns that I would like to understand better: NumVar: number of variants in the gene (or site) NumPolyVar: number of Polymorphic Genotypes What’s the difference? Thank you rvtests sequencing SNP • 9 views Login before adding your…

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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…

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negative PBS values

negative PBS values 0 Are negative values for the Population Branch Statistic (from Yi et al. 2010) meaningful? I obtained per SNP pairwise WC Fst from 3 populations of different sizes from Vcftools and calculated PBS. For some SNPs, the PBS is negative for a population and I am not…

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Calculating frequencies of possible combinations of SNP genotypes in a population

Hi all, I am looking to calculate the frequencies of all possible combinations of a group of SNP genotypes, in a population. This would be done based on the minor allele frequencies acquired in our population data. I just have a question on whether the following is the right way…

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Differences in HISAT2 indexes for download

Differences in HISAT2 indexes for download 0 Hi all, hope you guys are doing fine in the pandemic. So I have just recently beginning to move into computational biology stuff (and found it amazing) and one of the first things Im trying to do is to map fastq files against…

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Phasing with SHAPEIT

Edit June 7, 2020: The code below is for pre-phasing with SHAPEIT2. For phased imputation using the output of SHAPEIT2 and ultimate production of phased VCFs, see my answer here: A: ERROR: You must specify a valid interval for imputation using the -int argument, So, the steps are usually: pre-phasing…

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Validation in new sample

Validation in new sample 0 Hi Sam, I am trying to validate in a new sample a PRS I conceived by PRSice. I would like to ask if using snp_prs function (bigsnpr package in R) is a good way for that or should I use another tool or method. Best…

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Get gene names from rs SNP ids

Gene to rs id library(biomaRt) ## It might take long time to process if many genes (>50) in the list. ## hgnc_gene_symbols.txt is the file that has the list of gene symbols one per line. genes <- read.table(“~/hgnc_gene_symbols.txt”) ensembl = useMart(“ensembl”, dataset=”hsapiens_gene_ensembl”) dbsnp = useMart(“snp”, dataset = “hsapiens_snp”) getHGNC2ENSG =…

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Emergence and expansion of highly infectious spike protein D614G mutant SARS-CoV-2 in central India

COVID-19 laboratory screening Nasopharyngeal/Nasal/Oropharyngeal swabs in viral transport medium (VTM) received from acute phase patients with defined symptoms, asymptomatic cases with contact history with positive patients/ travel history were processed for laboratory confirmation of SARS-CoV-2 at Defence Research and Development Establishment, (DRDE) Gwalior, M.P., India. These samples were referred for…

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Bioconductor – systemPipeRdata

DOI: 10.18129/B9.bioc.systemPipeRdata     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see systemPipeRdata. systemPipeRdata: NGS workflow templates and sample data Bioconductor version: 3.9 systemPipeRdata is a helper package to generate with a single command NGS workflow templates that are intended to be used…

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Tajima’D and low-density SNP data

Tajima’D and low-density SNP data 1 Dear all, I am quite new to analysis of SNP data 🙂 My case is a bit particular because I only have genotypes from a few number of SNPs (~130) and more importantly, I do NOT have the associated DNA sequences because genotyping was…

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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…

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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…

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tabix for ID column

tabix for ID column 4 Hello, I’m looking for something similar to tabix. But instead of looking for informations within a given region, I would like to use the values in the ID column for quickly lookup. So for example I would like to take the compressed dbSNP file, index…

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The result of plink –freq is filled with NA

The result of plink –freq is filled with NA 0 I downloaded the vcf file. Then I used plink to convert it to a bed file and calculated the array frequency. However, the result of plink –freq was filled with NA. Can anyone give us an opinion? command ① ./plink –vcf…

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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….

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Annotate Structural variants with population specific allele frequency values

Annotate Structural variants with population specific allele frequency values 0 Hi, Has anyone tried filtering structural variants based on pupulation specific allele frequency (AF) values (for example gnomAD-SV or phase 3 1000 genome SV)? I have a set of SVs that I detected using a multipronged approach. For prioritising variants,…

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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…

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Manhattan plot how to reduce space between axis and axis-labels

Manhattan plot how to reduce space between axis and axis-labels 0 Hello everyone, I have plotted the Manhattan plot via qqman in R. However, it leaves huge white space between axis ticks and axis labels and also between axis labels and axis labs. Could someone offer any tip to reduce…

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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…

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How does one harmonize WGS data with Microarray data?

How does one harmonize WGS data with Microarray data? 0 Hello all, I’ve been working with microarray data which, of course, explicitly reports the genotype at each SNP on the microarray chip Now I am trying to incorporate WGS datasets into my project, and I would like to extract the…

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predixcan error

predixcan error 0 Hello, I am trying to run predict.py script from predixcan software But its showing error for me. The command use: python $PXCN_TOOLS/PrediXcan.py –model_db_path $MODELS/en_Whole_Blood.db –model_db_snp_key rsid –vcf_mode genotyped –vcf_genotypes $VCF_FILES/*.vcf –prediction_output $OUTPUT/GVDS_PrediXcan_Test_2021.txt the error: [E::bcf_hdr_parse] Could not parse the header, sample line not found Segmentation fault I…

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Ancestral polymorphisms shape the adaptive radiation of Metrosideros across the Hawaiian Islands

Significance Some of the most spectacular adaptive radiations of plants and animals occur on remote oceanic islands, yet such radiations are preceded by founding events that severely limit genetic variation. How genetically depauperate founder populations give rise to the spectacular phenotypic and ecological diversity characteristic of island adaptive radiations is…

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PRSice-2 without Ref SNP ID

PRSice-2 without Ref SNP ID 1 Does PRSice-2 support a base tile that has chromosome number/name and chromosome position instead of reference SNP ID in the base file? I’m trying to calculate PRS scores using a weights file from the PGS catalog with ~6 million variants. The file has only…

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Please help me understand linkage disequilibrium

I read many explanations about LD but I’m still not comfortable with the explanations. www.youtube.com/watch?v=iH8b-5BxtuY as you can see on these videos, most of them explains as if LD is about the relation between the genotype frequency of parental cell and gametes made from it. But if so, I should…

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Get rsID for a list of SNPs in an entire GWAS sumstats file

Here is a fairly efficient way to do this; assuming hg38 and BEDOPS and standard Unix tools installed. $ bedmap –echo –echo-map-id –delim ‘t’ <(awk ‘{n=split($0,a,/[:_]/); print “chr”a[1]”t”a[2]”t”a[2]+1″t”a[3]”https://www.biostars.org/”a[4];}’ sumstats.txt | sort-bed -) <(wget -qO- hgdownload.cse.ucsc.edu/goldenPath/hg38/database/snp150.txt.gz | gunzip -c | cut -f2-5 | sort-bed -) > answer.bed This gets around making…

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Rare variant association analysis (SKAT-O)

Hello everyone, I was wondering if it is statistically acceptable to perform SKAT-O analysis one a single gene. To elaborate, I am looking in a miRNA gene (80nt length) and I have found a small number of rare variants present in my case group, but none in my control group….

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Use of GenotypeGVCFs in population genetic studies

Use of GenotypeGVCFs in population genetic studies 0 I have 16 whole genome sequenced samples from two populations (8 for each population). My goal is detection of signature of selection and introgression. I performed read cleaning, mapping to reference, mark duplication. SNP calling was performed using HaplotypeCaller in GATK for…

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Joining the DNA dots to improve dairy breeding worldwide

Scientists from Agriculture Victoria, in collaboration with the University of Melbourne, have developed a world-first customised single nucleotide polymorphism chip designed with the latest known genes that affect dairy cattle traits. The work involves the customisation of a small piece of plastic — an SNP chip — with 50,000 small…

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High-throughput DNA sequencing of environmentally insulted latent fingerprints after visualization with nanoscale columnar-thin-film technique

. 2021 Sep;61(5):505-515. doi: 10.1016/j.scijus.2021.06.002. Epub 2021 Jun 7. Affiliations Expand Affiliations 1 Forensic Science Program and Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA. 2 Department of Psychiatry, Yale University School of Medicine & VA CT Healthcare System, New Haven, CT 06511, USA….

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Whole genome species clustering

I don’t think there is a “best” approach in your situation, given 1) the taxonomy of the group is probably still flaky. 2) being draft genomes, they probably are spotty and have sizeable gaps, and maybe even contaminants. Repeat regions are often left out of such assemblies. Actually, a good…

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Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection | Genome Biology

Stochastic Amplicon Ligation. DNA samples for oncology sequencing are typically extracted from FFPE tissues and can have average lengths of less than 500 nt due to accumulated chemical damage [18]. We developed the Stochastic Amplicon Ligation (SAL) method to enzymatically concatenate many short DNA molecules together to utilize the long-read…

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nanopore sequencing stock

It holds a 15% stake in the company and has valued its holding at £340m, giving a valuation of more than £2bn for the company. . While the company’s current shareholders have recorded its value at just over £2bn, analysts . Essay from the year 2011 in the subject Business…

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Bioinformatics Scientist | Washington, DC

Bioinformatics Scientist | Washington, DC | Kelly Services Location: Start New Search: bioinformatics scientistfluidicsbiodefensemicrobiomedna sequencingngsrnabioinformaticsnihsurgeglobal healthvaccineinfectious diseasecomputationalallergymicrobiologymachine learningclinical researchbethesdahiv aids Kelly ServicesWashington, DC Full-time Perform a wide variety of complex procedures and techniques in support of RTB including Affymetrix fluidics and hybridization protocols; high-throughput TaqMan processing; microarray data analysis; high-throughput…

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wont recognize the gtf or gff3 files (runtime exception)

snpeff : wont recognize the gtf or gff3 files (runtime exception) 1 Hi, I am trying to build a custom databasee for snpeff. As instructed both in the forum and snpeff instructions, I did the following; Then I added the following into snpEff.config file # BG94_1 BG94_1.genome : BG94_1 Then…

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VCFtools doesn’t keep any variants using GATK output

Hi guys! I’m having trouble using vcftools to filter snp through GATK output. For infomation, i used the command HaplotypeCallerto make SNP-calling of 12 samples ; i used the CombineGVCFs to join the 12 VCFS and make the joint call after merging the vcf files; i used the VarianFiltration for…

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