Tag: SnpEff

SnpEff does not create htmlStats 0 SnpEff does not create htmlStats with the below command: $ snpEff eff -Xmx20G LAB330 LabUsa16cWild01-20_L-Q.vcf | head ##fileformat=VCFv4.0 ##filedate=20210414 ##source=SGSautoSNP ##reference=NbLab330.genome.softmasked.fasta ##phasing=allhomozygote ##INFO=<ID=DP,Number=1,Type=Integer,Description=”Read depth over all samples”> ##INFO=<ID=PL,Number=0,Type=String,Description=”Panel”> ##SnpEffVersion=”5.0e (build 2021-03-09 06:01), by Pablo Cingolani” ##SnpEffCmd=”SnpEff LAB330 LabUsa16cWild01-20_L-Q.vcf ” ##INFO=<ID=ANN,Number=.,Type=String,Description=”Functional annotations: ‘Allele | Annotation…

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…

1. Latgé, J. P. and Chamilos, G. Aspergillus fumigatus and Aspergillosis in 2019. Clin. Microbiol. Rev. doi.org/10.1128/CMR.00140-18 (2019). 2. Invasive Aspergillosis. LIFE www.life-worldwide.org/fungal-diseases/invasive-aspergillosis (2020). 3. Harrison, N. et al. Incidence and characteristics of invasive fungal diseases in allogeneic hematopoietic stem cell transplant recipients: a retrospective cohort study. BMC Infect. Dis….

When I annotated a human genome using reference genome with snpeff, at each genomic position, there are more than one annotation results in the same gene and also other genes appearing and they are separated by “,”. Here is an example below at a genomic position of 204,688,055 on chromosome…

error while annotating vcf file using snpEff 0 I want to annotate my vcf file with geneid of ensemble. I used snpEff tool to annotate vcf file with geneID of ensemble. But in my case its the same gene ID being assigned for every rsid. This is the command I…

I just went through figuring this out and I thought I would add my process, including the FASTA component, using Vibrio phage VP882 as my example and utilizing the gff strategy you mentioned in a comment to the other answer. Here is everything I did using an established snpEff installation….

Obtain heterozygous variant frequencies from dbNSFP using snpsift 0 Dear colleague, I am using the dbNSFP (v4.2a) database to annotate the variants identified in WGS (homo sapiens) using snpsift. Unless I am mistaken, I cannot find the parameters to get heterozygous variant frequencies of gnomad from dbNSFP (v4.2a). I only…

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

Construction of the reference genome database (GCA_000001405.15_GRCh38) with snpeff 1 Dear colleagues I used the reference genome GRCh38 version GCA_000001405.15_GRCh38 / seqs_for_alignment_pipelines.ucsc_ids downloaded from ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/ This version was used for alignment and variant calling, however, I wanted to annotate genetic variants by snpeff v5. I did not find this version…

Missing some predictions based on dbNSFP v4.2a 0 Hello everybody, I used dbNSFP v4.2a database for functional prediction and variant annotation. As mentioned in the download site sites.google.com/site/jpopgen/dbNSFP, this version compiles prediction scores from several prediction algorithms (SIFT, SIFT4G, Polyphen2-HDIV, Polyphen2-HVAR. ….), and other information, including allele frequencies observed in…

Hello, I’m trying to annotate variations in NGS data from bacterial artificial chromosomes with respect to the reference sequence. To do this i build a map of the BAC (including vector) and map the NGS reads to this BAC map. I also use a variant caller to find any differences…

Introduction Pediatric tuberculosis (TB) is a significant global health threat and is one of the top ten causes of death in children.1 Globally, in 2019, an estimated 10.0 million people fell ill with TB, with children (aged under 15 years old) accounting for 12%, causing 1.4 million deaths.2 With the…

snpeff warning cannot find last exonic position before transcript 1 hi, everyone! when i buliding database by commmand “java -jar /opt/snpEff/snpEff.jar build -v purdomii” it report warning information: WARNING: Cannot find last exonic position before 1237583 for transcript ‘Popu0001410.1’ WARNING: Cannot find last exonic position before 2405626 for transcript ‘Popu0002640.1’…

filter multiple VCF files using snpSift 1 Hi, I have several hundreds annonated VCF files (annotated using snpEff). I want to filter out all the low quality and low impact variants in all VCF files. Is there a way to  filter all files at one time, rather than filtering each…

Issues generating the annotated.eff.vcf file : Sanity check his should never happen 0 Hello, I am having a hard time deciphering the error associated with the vcf annotation file. I used the command: java -Xmx8g -jar snpEff.jar Tair10.1 /globalhome/cae453/HPC/sample6.vcf > /globalhome/cae453/HPC/sample6.eff.vcf The output is java.lang.RuntimeException: Sanity check: This should never…

S. cerevisiae in snpEff databases 0 On snpEff 5.0, if you do java -jar snpEff.jar databases and look for Saccharomyces cerevisiae, you will find (among many other entries): R64-1-1.75 Saccharomyces_cerevisiae snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_R64-1-1.75.zip R64-1-1.99 Saccharomyces_cerevisiae snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_R64-1-1.99.zip Saccharomyces_cerevisiae Saccharomyces_cerevisiae snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_Saccharomyces_cerevisiae.zip The entry that is simply named Saccharomyces_cerevisiae — what is it? Is it…

Hello, I have 2 types of VEP annotated VCF file – regular vcf and gnomad genome file. I would like to extract counts of both missense, synonymous, upstream and intron variants for each gene in each file. Output should be something similar to this: MHTFR: missense 23, intron 100, synonymous…

Question: Reference genome version between variant calling and annotation 0 Dear colleagues, My project is focused on the annotation of human genetic variants (SNPs and short InDels) of WGS and WES. I am using SNPEff version 5.0. In the snpeff config file I found GCA_000001405.28_GRCh38.p13 Homo sapiens (hg38) (UCSC). In…

Running SnpSift in parallel 0 Hi, I am trying to using SnpSift to calculate case vs control groups. The file I am using is quite large and the first time I ran SnpSift on the file took quite a few days to finish. I am in a bit of a…

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…

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…

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…

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…

    Significance To date, the potential of utilizing root traits in plant breeding remains largely untapped. In this study, we cloned and characterized the ENHANCED GRAVITROPISM2 (EGT2) gene of barley that encodes a STERILE ALPHA MOTIF domain–containing protein. We demonstrated that EGT2 is a key gene of root growth…

Case Control count per variant 0 Hi, I was wonder if there was any software out there that will count the number of samples in a group that are homozygous ref, heterozygous, or homozygous for a variant an output result in a text file? In the past, I have been…

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 |…

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…