Tag: FreeBayes

Building reference dbSNP file using WGS samples 2 Dear scientific community, I have to call variants from WGS samples of citrus. I used GATK pipeline for post processing of aligned reads but reference dbSNP file is not available for citrus sinensis. I am using bootstraping method. Removed duplicates and called…

Tool for structural variation detection of plant WGS data 1 Dear all, I have been calling SNPs and indels from WGS data but I have never performed structural variation calling. Please suggest any tool to identify structural variations from plants WGS data. Does freebayes facilitate this? Looking for your valuable…

Hey everybody, I have just performed the alignment of paired-end reads to a reference using bwa mem with the -M flag, ran samtools markdup and flagstat. Flagstat produced the following output: 4985084 + 0 in total (QC-passed reads + QC-failed reads) 1806492 + 0 primary 3178592 + 0 secondary 0…

Challenges in Variant Calling and Genotyping with Short-Read Data Mapped to a Pangenome Graph: Seeking Guidance 0 Hello all, We are reaching out since we have some practical questions regarding variant calling and analyses of short-read data mapped to a pangenome graph. We are working on a project aimed to…

Building reference dbSNP file for citrus sinensis using 80 WGS samples 1 Dear scientific community, I have to call variants from 80 WGS samples of citrus. I used GATK pipeline for post processing of aligned reads but reference dbSNP file is not available for citrus sinensis. I am using bootstraping…

Bootstrapping for BQSR of 80 WGS samples 0 Dear scientific community, I have to call variants from 80 WGS samples of citrus. I used GATK pipeline for post processing of aligned reads but reference dbSNP file is not available for citrus sinensis. I am using bootstraping method. Removed duplicates and…

Population and clinical samples The province of Alberta has a population of approximately 4.4 million. During July 19 to December 31, 2022 (the period of this study), molecular testing for SARS-CoV-2 was performed for individuals at risk for severe illness who would benefit from early treatment with antivirals, healthcare workers,…

Position: Bioinformatics Data Analyst Company: GenomicStar – A SaaS based Precision Medicine Platform Job Purpose: The Bioinformatics Data Analyst will play a critical role in the development, validation, and implementation of data analysis pipelines for various genetic test panels, incorporating state-of-the-art AI techniques. This role is integral to our commitment…

We are now going to call variants with two different approaches from the files we have been working with all course. Please use the following files, parameters, and listed versions of the software for this assignment. We will use the reference Ebola genome: /data/compres/refs/AF086833.2.fasta And this set of paired-end sequences:…

Mice All animal use was approved by the Department of Comparative Medicine at the Massachusetts Institute of Technology (MIT) and the Institutional Animal Care and Use Committee under protocol no. 0714-076-17. Mice were housed with a 12-h light/12-h dark cycle with temperatures in the range 20–22 °C and 30–70% humidity. KrasLSL-G12D…

Introduction nf-core/sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses. The pipeline is built using…

News:Virtual Variant Detection Workshop: September 11-14, 2023 0 Virtual Variant Detection Workshop Dates: September 11-14, 2023 (4 days) Time: 9.00am – 12.00pm Location: Online Cost: $400 (UConn affiliates including UConn Health) $500(External Participants) The workshop will cover an introduction to linux and high performance computing, an introduction to variant detection,…

Introduction Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), continues to pose a significant global public health challenge.1–3 In 2021, there were 10.6 million new TB cases worldwide, with China accounting for 780,000 cases, making it the third highest burden country for TB globally.4 The World Health Organization (WHO) estimates that…

Problems with bcf concat 1 Hello! I have multiple VCFs files for the same sample. I used the commad bcftools concat -a -Oz -o concat.vcf.gz 242487_vs_242482.bcftools.vcf.gz 242487_vs_242482.freebayes.vcf.gz But i have the next error Checking the headers and starting positions of 2 files [W::hts_idx_load3] The index file is older than the…

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, and was edited by Istvan…

I would like to double check whether to use VCF concatenate or VCF merge on my chromosome files. I have done SNP calling using FreeBayes, but split this by chromosomes in order to call SNPs in parallel. I also split some particularly large chromosomes by chromosome position with no overlap,…

The Research Informatics (RI) Bioinformatics group within the University of Minnesota Supercomputing Institute (MSI) is hiring a full-time Bioinformatics Analyst to support basic biomedical and applied clinical genetic research for the Department of Laboratory Medicine and Pathology (LM&P) at the University of Minnesota. The analyst in this position will…

Proper Bowtie2 settings for snp calling applications 1 Hi, I’d like to map illumina paired-end reads to the reference genome by Bowtie2 for downstream snp calling with Freebayes. The reads are already adapters and quality trimmed. I plan to specify the following Bowtie2 options: –end-to-end –very-sensitive –no-mixed –no-discordant I’m wondering…

26All paired-end Illumina libraries were inspected with FastQC v0.11.5() and trimmed and filteredwith Trimmomatic v0.36 (66). Read mapping was performed with sppIDer pipeline(81) using a combined reference including the genome assembly of CBS9595 (asrepresentative of P1 lineage, Supplementary File 1 for more details) and CBS14141(as representative of P2 lineage, Supplementary…

vcftools – Fst statistics 1 I have .vcf file with over 78 000 variations in 95 experiment subjects. I used vcftools to exctract fixation index score for general differentiation between Case and Control groups. ./vcftools –vcf SCH_freebayes_sort_ostE_SnpEff_SnpSift.vcf –weir-fst-pop Case.txt –weir-fst-pop Control.txt –out FstExon_Case_vs_Control After filtering, kept 95 out of 95…

Unable to find FASTA index entry for ‘/mountpoint/fastQ/Homo_sapiens_assembly38-3.sorted.bed.gz’ 1 I’m trying to use freebayes to call variants through the following parameters : freebayes -f $REF -r $REGIONS -b 03.align/$FQ.align.sort.marked.bam > 04.freebayes/$FQ.var.vcf The error reports: unable to find FASTA index for bed file. I have both .fasta and .fasta.fai file and…

Hi there, I am new in SNP analyses so before starting doing anything I would like to check if my pipeline is correct. What I have now is : RNA-seq samples (.fq.gz) + Trinity assembly (from those reads). My model organism has not an assembled genome, that’s the way I…

Wanyang Dong,1,* Qi Peng,1,* Xiaohua Tang,1,2,* Tian Zhong,1 Shunan Lin,1 Ziling Zhi,1 Jingyi Ye,1 Bixia Yang,1 Ning Sun,1,3 Wenchang Yuan1 1Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, People’s Republic of China; 2Third Affiliated Hospital…

Schematic representation of the experimental design. a Experimental conditions. Three experimental conditions were tested: WT and HR strains growing without drug challenge, and HR strains growing under drug challenge. Four types of samples were evaluated per experimental condition (input, monosome, light polysomes, and heavy polysomes). The experiment was done in…

How is it different from typing the same into ChatGPT? And it does not take 2-3 minutes … Can you give me two variant callers? Sure, variant callers are bioinformatics software tools used to identify variants (like SNPs and indels) from sequence data. Here are two commonly used variant callers:…

Can you share some of the image as text for easier understanding? It seems like there might be an issue with your BAM file or the region you are trying to call variants on. To help diagnose the issue, please follow these steps: 1. Check if your BAM file is…

I am trying to run a snakemake pipeline with packages installed from a main.yml file. One of the dependencies of the package is samtools, Previously, having the dependency listed as samtools did not seem to run into any problems. The actual yml file is: name: yevo_pipeline_env channels: – defaults -…

Variant Calling with Multiple Individuals in Freebayes 1 Hello, I am currently a new student in Bioinformatics and was trying to do variant calling with Freebayes software. I have 10 individuals and also have a reference genome. I have already sorted and indexed all my .bam files ready for variant…

How to fix FreeBayes error “unable to find FASTA index entry for bed files” 0 I’m trying to use freebayes to call variants through the following parameters using RNA-Seq data: $freebayes –fasta-reference $ref \ –region $BED \ $bam \ ${outdir}/${sample}.freebayes.vcf and my bed files like this: chr1:11868-12227 chr1:12612-12721 chr1:12974-13052 chr1:13220-14501…

Outgroup for plastome NJ-tree (from pseudoalignment based on SNPs) 0 Good morning, I have whole-genome sequencing data for several samples of one plant species. I performed mapping of all reads on the merged nuclear+plastid+mitochondrial reference genome of this species (bwa-mem2), extract part of the alignment, that was refered to plastome,…

Why 0/0 genotype refers to SNP and ALT != REF (in vcf file after freebayes) 1 Good morning, Could you please explain me, why 0/0 genotypes in vcf are SNPs? According to this description of GT: 0/0 the sample is a homozygous reference 0/1 the sample is heterozygous (carries both…

reference for freebayes or samtools mpileup after extracting chromosome from alignment 1 Good evening, I have extracted one chromosome from alignment map (.bam), using samtools view: samtools view -b map.bam chr1 > map_chr1.bam Now I would like to perform SNP calling using freebayes. Is it correct to use chr1.fasta as…

Next-generation sequencing (NGS), which makes millions to billions of sequence reads at a fast rate, has greatly sped up genomics research. At the moment, Illumina, Ion Torrent/Life Technologies, 454/Roche, Pacific Bioscience, Nanopore, and GenapSys are all NGS platforms that can be used. They can produce reads of 100–10,000 bp in…

SV tool recommandation for detecting 50bp> deletion sequence 0 Hello. I am a 1st year grad student in genetics lab. I am new to bioinformatics. computer: MS-Linux ubuntu-miniconda3 data: fish tissue gDNA NGS(MGISEQ,, 150 paried end read) picard bam, bai file My goals are 1. compare sample seq with NCBI…

Error: Please supply a reference FASTA/GBK/EMBL file with –reference 0 Hi, i am trying to run snippy on multiple genomes, however it gives following error like Please supply a reference FASTA/GBK/EMBL file with –reference even after providing the reference file. i don’t understand why it is happen and here is…

Details Posted: 13-Aug-22 Location: Minneapolis, Minnesota Salary: 43944.32 – 123022.07 Categories: Research Support – Laboratory/Non-Laboratory Staff/Administrative Additional Information: 2 openings available. The Research Informatics Solutions (RIS) group within the University of Minnesota Supercomputing Institute (MSI) is hiring two full-time Bioinformatics Analysts to support research at the University of Minnesota. Analysts…

Context: I’m trying to call variants on a sequencing project using pooled genotyping-by-sequencing. Pools consist of 94 samples each, alongside a number of individuals. Sequence data was demultiplexed and then aligned to a reference genome using hisat2, and the resultant bams were merged with samtools merge. The problem bam is…

I received (from manufacturer) several .bam files and I used four callers (samtools, freebayes, haplotypecaller, deepvariant) to find some sequence variants. In obtained .vcf files, I took a closer look to some calls. I found interesting, homozygous one rs477033 (C/G Ref/Alt) with flag ‘COMMON=0’ and very low MAF. I also…

Hi Lucas, got a weird one for you. If I change the caller from hapotypecaller to freebayes, I get the error below. It’s doubly strange because it seems to occur well before freebayes would be used in the pipeline. [Sat Dec 11 11:13:02 2021] rule samtools_stats: input: dedup/111D03-1.bam output: qc/samtools-stats/111D03-1.txt…

Procambarus fallax collections and PCR genotyping Animals were collected from various wild populations (Table S1) in compliance with state and local regulations (Georgia department of natural resources scientific collection permit 115621108, state of Florida collection permits S-19-10 and S-20-04). DNA was isolated from abdominal muscle tissue using SDS-based extraction and precipitation…

Significance Small and isolated populations have low genetic variation due to founding bottlenecks and genetic drift. Few empirical studies demonstrate visible phenotypic change associated with drift using genetic data in endangered species. We used genomic analyses of a captive tiger pedigree to identify the genetic basis for a rare trait,…

Exctracting amino acid substitutions 0 Good day, I’m trying to develop a pipeline to determine mutations which are responsible for amino acid changes in genes associated with antibiotic resistance. I have roughly 300 bacrtial isolates. My approach so far has not been fruitful, in short this is what i tried:…

Hey, I am looking for a way to add samples ID names to the FORMAT in my vcf file. I have 10 sorted Bam files. I used Freebayes to create vcf files and my next step is merging all 10 files for VcfSampleCompare. And for that I need to define…

FreeBayes Error 0 Hi- I am trying to use FreeBayes to identify polymorphic sites and it will not run. It keeps throwing this error “unable to find fasta index entry for GL630349”. Does anyone know what to do in this situation? Thank you Galaxy Coursera FreeBayes Polymorphisms • 16 views…

VCF Filter On Small Genomes 0 Hi guys, I am working on a yeast species (Candida glabrata) NGS data to find any mutations related to drug resistance. I am new in bioinformatics so I am using Galaxy.eu to get use to algorithms. There is literature about some genes that mutations…