Tag: VEP

Hi all! I annotated a VCF file using VEP and noticed that it reports several variant IDs to each input variant. For example, this is an excerpt of one of the variant lines (I removed the annotation info that is not relevant to the question): 12 25398284 . C A…

The UKB is approved by the North West Multi-centre Research Ethics Committee (www.ukbiobank.ac.uk/learn-more-about-uk-biobank/about-us/ethics). The current study was conducted under UKB application no. 26041. The data in the UKB were collected after written informed consent was obtained from all participants. The Human Research Committee of the MGB approved the Biobank research…

VCF file will be having seven fixed columns and INFO column. Chromosome, position, ID, ref, alt, qual, filter, and INFO column. This INFO column will be having the variant related information. In the INFO column CSQ field will be having multiple fields – 82 fields fixed with the delimeter “|”…

I am trying to reproduce an analysis result, and there is a requirement regarding the format of the result: the ‘3’ rule ‘: all mutations should be expressed in a position close to the end of the gene transcription direction (3’ end). The result I obtained is(annotate from VEP) Chromosome…

Newest ‘vep’ Questions – Stack Overflow …

Dear Biostars, I am having a confusing issue with my CADD plugin. This is confusing because when I run VEP for my whole trio – all the plugins work fine. However when I try to run CADD for individual – pivoted files – it no longer does and I get…

You can check out these services: * myvariant.info/v1/api#/ * api.ncbi.nlm.nih.gov/variation/v0/ * rest.ensembl.org/#VEP As far as I know they all return JSON. You can check out a tool like jq or a package in your fav language to parse JSON. **Example:** curl -s ‘rest.ensembl.org/vep/human/id/rs2656176?’ -H ‘Content-type:application/json’ | jq ‘.[].colocated_variants[].frequencies’ { “A”:…

We are seeking a bioinformatician with significant oncology or immunology experience to join a multidisciplinary team developing leading-edge genomics analysis tools to understand the immune system’s response to cancer. This highly motivated, detail-oriented individual would join a clinical genomics analysis group and will be responsible for developing and applying bioinformatics…

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 am trying to install PhyloCSF: github.com/mlin/PhyloCSF Since it is needed for new VEP99. In order to do that I needed to install ocaml, bubblewrap, opam. Second bullet point: opam install batteries ocaml+twt gsl Did not work, but I found that this one works: opam install ocaml-twt As can be…

How to install VEP plugins in conda environment 1 I installed VEP through miniconda and use VEP through my conda environment. I would like to install VEP plugins (ex, CADD), but I do not have the INSTALL.pl script VEP instructs to use to install plugins (I think this is because…

Haploview Error 0 I would like to request for help for the following. When I am giving input of ped and info file generated from plink into haploview. I am getting an error. “File does not any zero valid indiviuals” I am thankful in advance plink Haploview vep • 36…

adding transcripts ID to the REVEL score 0 I am annotating variants for clinical diagnosis. One of the data required by my team is REVEL. We work with specific transcripts so when clinicians do variant interpretation, they need to check if our preferred transcript is among the transcripts considered. REVEL…

VEP tool 0 I am using VEP tool for variant annotation, I ran the VEP command : ./vep -i sample.vcf -o out.txt –offline but it shows the following error : ——————– EXCEPTION ——————– MSG: ERROR: Cache directory /home/shweta/.vep/homo_sapiens not found STACK Bio::EnsEMBL::VEP::CacheDir::dir /home/shweta/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:305 STACK Bio::EnsEMBL::VEP::CacheDir::init /home/shweta/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:219 STACK Bio::EnsEMBL::VEP::CacheDir::new /home/shweta/ensembl-vep/modules/Bio/EnsEMBL/VEP/CacheDir.pm:111 STACK…

Mehari is a software package for annotating VCF files with variant effect/consequence. The program uses hgvs-rs for projecting genomic variants to transcripts and proteins and thus has high prediction quality. Other popular tools offering variant effect/consequence prediction include: Mehari offers predictions that aim to mirror VariantValidator, the gold standard for…

Hi, I’ve been asked to semi automate (as far as full automation of the process seems to be impossible) the ACMG annotations of WGS data for our clinicians. What are the options here? I’ve checked several: varsome (paid full access, closed code) InterVar (seems nice, but works only with annovar,…

What does the decimal ending of a transcript id mean? 1 When working with alternative transcripts, I see a decimal ending to the transcript id. What does the decimal value add to the transcript meaning? For example, a mutation, BRAF p.V600M is annotated by VEP with: csn=”ENST00000479537.1:c.82G>A_p.Val28Met” hgvsc=”ENST00000479537.1:c.82G>A” transcript_id=”ENST00000479537″ &…

VCF file generated by Gridss not recognised by VEP 0 Hello, Currently, I am engaged in analyzing genomic Next-Generation Sequencing (NGS) data as a part of my professional activities. Specifically, I am attempting to integrate the Gridss tool into my workflow for the purpose of variant calling (indels). Unfortunately, I…

Easy way to split VCF file by chromosome 2 Hi, Im trying to submit a job on the TOPMED/Michigan imputation server, but it returns an error saying that I need to split my VCF by chromosome Is there an easy way to do this? Will bcftools help? sequence TOPMED chromosome…

I have a vcf files like below: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT treatmentSample chr1 857100 . C T 1756.06 PASS AC=2;AF=1;AN=2;DP=60;ExcessHet=3.0103;FS=0;MLEAC=2;MLEAF=1;MQ=60;QD=29.27;SOR=1.812;CSQ=chr1:857100|T|SNV|ENSG00000228794|ENST00000445118|LINC01128||1|MODIFIER|non_coding_transcript_exon_variant||||5/5|||||||||||||||||| GT:AD:DP:GQ:PL 1/1:0,60:60:99:1770,180,0 Does anyone know how to seperate INFO columns into different columns? And also how to separate treatmentSample column following the FORMAT ORDER? I…

Fasta file and GTF file for STAR alignment 3 Hello there, The top-level fasta file will include chromsomes, regions not assembled into chromosomes and N padded haplotype/patch regions. See more here: ftp.ensembl.org/pub/release-92/fasta/mus_musculus/dna/README. If you are only looking for reference genome assembly chromosome level sequences then use the primary_assembly.fa file. The…

Variant effect predictor in ictalurus punctatus 0 Hello everyone I performed a VEP analysis today using a catfish reference genome and my VCFs are from the species Pimmelodus Yuma. The problem is that the predictors did not give me any results in the missense variants. Is this normal? Here are…

Ensembl Variant Effect Predictor (VEP) VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as …… Read more > The GA4GH Variation Representation Specification (4) Context precision: VRS does not lump together or link variation contexts; a variation…

Availability of information on genes in Gnomad VCF data 1 Hi , Im new to gnomad and genetics in general and i was wondering does the gnomad genome data that is downlaoded in the vcf format on variants contains information of what is the nearest gene and is the genomic…

BioPerl 1.7.2-GCCcore-8.2.0-Perl-5.28.1 There is a newer version of BioPerl Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. Accessing BioPerl 1.7.2-GCCcore-8.2.0-Perl-5.28.1 To load the module for BioPerl 1.7.2-GCCcore-8.2.0-Perl-5.28.1 please use this command…

Installing ensembl-vep 1 Hello all , I tried installing ensembl-Vep on mu ubuntu using following commands git clone github.com/Ensembl/ensembl-vep cd ensembl-vep perl INSTALL.pl I got the error as :- ERROR: DBI module not found. VEP requires the DBI perl module to function I tried installing DBI etc but the error…

hgmd variants from Ensembl 0 I know that Ensembl has hgmd variants amongst other annotations as given here: hgmd variants How can I download these variants from Ensembl? I downloaded VEP because it uses multiple tracks including HGMD: VEP Is it possible to use VEP to extract just the HGMD…

Unexprected Ensembl-vep results 0 Hi.I got a VCF from an individual that shows symptoms of a known disease with known mutations. I run it with Ensembl-vep, expecting to find some of those mutations in the results, yet, all the consequences in the results are “intergenic-variant”.The command I used was: –cache…

annotation_file ##INFO=<ID=ClinVar_CLNSIG,Number=.,xxx ##INFO=<ID=ClinVar_CLNREVSTAT,Number=.,yyy ##INFO=<ID=ClinVar_CLNDN,Number=.zzz #CHROM POS ID REF ALT QUAL FILTER INFO chr1 10145 . AAC A 101.83 . AC=2;AF=0.067;AN=30;aaa chr1 10146 . AC A 98.25 . AC=2;AF=0.083;AN=24;bbb chr1 10146 . AC * 79.25 . AC=2;AF=0.083;AN=24;ccc chr1 10439 . AC A 81.33 . AC=1;AF=0.008333;AN=120;ddd chr1 10450 . T G 53.09…

stay In the first two sections , We compared the differences vcf Use of annotation software , And convert the demerit recorded after the annotation into maf File format , because snpeff The comment result cannot be converted to maf, So we will compare later ANNOVAR、VEP、GATK Funcatator The results of…

dint May 9, 2022, 1:33pm #1 i’m just wondering if you can specify cadd, gnomad, clinvar and dbNSFP options when annotating with hail on dxjupyterlab_spark_cluster o the UKB RAP? From the hail website, the following command can be used on your matrix file to annotate with these features: db =…

Details Posted: 22-Apr-22 Location: Danville, Pennsylvania Type: Full Time Salary: Open Categories: Operations Job Summary Primary accountability is to leverage the organization’s data assets exome sequencing data (>180,000 individuals) from MyCode Community Health Initiative to improve quality, efficiency and generate knowledge specifically in the field of bioinformatics within health research….

Error occurence after merging files with bcftools: wrong number of fields ? 1 I have multiple vcf of CASES and CONTROLS variations annotated by VEP, SNPEff, SnpSift. first pair vcf -> only variations| CASES and CONTROLS second pair vcf -> variations + SnpEff | CASES and CONTROLS third pair vcf->…

Hello, I used and edited the command line to use –vcf to import vcf file. I used these commands: for chr in $(seq 1 22); do      plink –vcf /dbGAP/GTEx_Analysis_2017-06-05_v8_WholeExomeSeq_979Indiv_VEP_annot.vcf.gz            –chr $chr            –recode            –out…

Here we demostrate several in vivo tests (flash visual evoked potential, pattern electroretinogram and optic coherence tomography) in goat and rhesus macaque to understand the structure and function of the optic nerve and its neurons. Hi, everyone. This is Yikui Zhang from Wenzhou Eye Hospital. The upper nerve lacks Exxons…

I’ve annotated some variants using VEP, and was looking at the minor allele frequencies. Some of the variants had very different MAFs in the annotation than I expected (I expected MAF < 1%, whereas some annotated MAFs were >50%). I looked up the same variants on the gnomAD v3 browser,…

I’ve installed vep in conda like so: conda install ensembl-vep=105.0-0 And then I installed the human cache like so: vep_install -a cf -s homo_sapiens -y GRCh38 -c /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/refs/vep –CONVERT But when I try and run vep I get an error: vep –dir_cache /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/refs/vep -i /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/cohort.norm_recalibrated.vcf -o /mnt/gpfs/live/rd01__/ritd-ag-project-rd018o-mdflo13/data/test/manual/results/variants/cohort.norm_recalibrated_vep.vcf Am I doing…

vep -i examples/homo_sapiens_GRCh38.vcf –database Can’t locate Bio/PrimarySeqI.pm in @INC (you may need to install the Bio::PrimarySeqI module) (@INC contains: /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/modules /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0 /home/youssef/anaconda3/envs/ngs1/lib/site_perl/5.26.2/x86_64-linux-thread-multi /home/youssef/anaconda3/envs/ngs1/lib/site_perl/5.26.2 /home/youssef/anaconda3/envs/ngs1/lib/5.26.2/x86_64-linux-thread-multi /home/youssef/anaconda3/envs/ngs1/lib/5.26.2 .) at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Slice.pm line 75. BEGIN failed–compilation aborted at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Slice.pm line 75. Compilation failed in require at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Feature.pm line 84. BEGIN failed–compilation aborted at /home/youssef/anaconda3/envs/ngs1/share/ensembl-vep-88.9-0/Bio/EnsEMBL/Feature.pm…

Fail to install Ensembl VEP 2 Hello I have been encounter some issues on installing the Ensembl VEP. I am using Ubuntu 20.04 system, with the newest perl v5.34. perl -MBio::Root::Version -e ‘print $Bio::Root::Version::VERSION,”n”‘ 1.006924 However, when I install the VEP, it failed. Hello! This installer is configured to install…

Describe the issue VEP give errors even my query and reference has same assembly version Command :$: ./vep -i examples/homo_sapiens_GRCh37.vcf –cache –refseq cache reference details while running install.pl ? 458 NB: Remember to use –refseq when running the VEP with this cache! downloading ftp.ensembl.org/pub/release-104/variation/indexed_vep_cache/homo_sapiens_refseq_vep_104_GRCh37.tar.gz unpacking homo_sapiens_refseq_vep_104_GRCh37.tar.gz converting cache, this may…

Installing Bio::DB::Big::File on Ubuntu (Building and testing…) 0 Hi everyone, I’m trying to install VEP, I already downloaded all the recommended PERL libraries/dependencies/modules But I still have a problem with Bio::DB::Big::File and Bio::DB::Big::AutoSQL They asked for lib big wig. I’ve found three ways to install this (in my understanding): sudo…

Failed to instantiate plugin dbNSFP in VEP 0 Hi Team, My VEP (version 105, installed by perl INSTALL.pl) works well. But I face some problems to use dbNSFP plugin (also installed by perl INSTALL.pl) with VEP tool. My dbNSFP version 4.2a was installed by the following code without any warning…

I’m trying to install VEP in a conda environment, but it keeps failing. I’ve tried with the normal installation process: conda install -c bioconda ensembl-vep But get the below errors which run for about an hour and eventually fail: $ conda install -c bioconda ensembl-vep Collecting package metadata (current_repodata.json): done…

Conda failing to install VEP 0 I’m trying to install VEP in a conda environment, but it keeps failing. I’ve tried with the normal installation process: conda install -c bioconda ensembl-vep But get the below errors which run for about an hour and eventually fail: $ conda install -c bioconda…

Failing to install VEP dependencies 0 I’m trying to install VEP, but am getting stuck installing its dependencies. I try to install as suggested here www.ensembl.org/info/docs/tools/vep/script/index.html cd ~/bin git clone github.com/Ensembl/ensembl-vep.git cd ensembl-vep perl INSTALL.pl But I get this error: ERROR: DBI module not found. VEP requires the DBI perl…

how do you get an IN-FRAME deletion stop gain variant? 1 I was looking through annotaitons for variants in my genomics data and I saw some variants being labeled by VEP derived ensembl consequence as “stop_gained&inframe_deletion” How do you get a stop gain from an inframe deletion? It makes sense…

Including tbi file along with VCF when running VEP on remote dataset (GnomadV3) 0 Hi, I am trying to run VEP on remote data from GnomadV3. I was hoping to run it remotely, without the need to download the dataset. However, when I try to run it remotely, I get…

.vcf to.csv conversion 4 Hi, I have uploaded some WES .vcf files to the ensembl VEP for analysis but am unable to download the results as the usual excel file format due to the large file size, I can only download the .vcf file. Does anyone know of a tool…

Deleted:Getting an error regarding the reference length and coordinates when using Ensembl-vep 0 Hello.The input that was submitted to Ensembl-vep’s API was in the following format: 12 9067664 9116229 A/C – 12 9067664 9116229 A/G – 12 9067664 9116229 A/T – The command was ensembl-vep/vep –database -i /input/variants.txt -o output/output.txt…

Running a Linux command for “Ubuntu on Windows” with WSL from a python script 1 Hello.I’m using the command Popen([‘wsl’, ‘/tmp/docker-desktop-root/mnt/host/c/Users/user/ensembl-vep/vepn’], stderr=STDOUT).stdout from a python script to run a Linux program “ensembl-vep”. Unlike when I run the command in “Ubuntu on Windows”, when I run it from the python script…

Functional annotation with VEP: combine the same variant between the samples in the same line (question) 0 Dear colleagues I used VEP to annotate a multisamples vcf file, but I get separate lines of the same variant, which corresponds to each sample. here is an example of output Location Allele…

Error when trying to use Ensembl virtual machine 0 Hello. After realizing that installing Ensembl-vep on Windows requires installing multiple other programs, I tried using the Ensembl Virtual Machine. I followed the instructions at www.ensembl.org/info/data/virtual_machine.html, and when I ran the virtual machine I got the following error message: I tried…

doi: 10.1002/humu.24298. Online ahead of print. Sarah E Hunt  1 , Benjamin Moore  1 , Ridwan M Amode  1 , Irina M Armean  1 , Diana Lemos  1 , Aleena Mushtaq  1 , Andrew Parton  1 , Helen Schuilenburg  1 , Michał Szpak  1 , Anja Thormann  1 , Emily Perry  1 , Stephen J Trevanion  1 , Paul Flicek  1 , Andrew…

vcf – Ensembl Variant Effect Predictor (VEP) issue during execution – Bioinformatics Stack Exchange …

Hi all, I am using Ensembl VEP (command line) to annotate a VCF I have. I am specifically looking for gnomAD allele frequencies, which is fairly straight forward to do, technically speaking. However, the data looks off in some cases. For example, when I pass in: 10 69408929 COSM3751912 A…

Ensembl FTP Mirror in USA? Slow Downloads 1 Hello I work on a fairly good cluster at an R1 university in the USA. I am downloading the VEP 101 indexed cache files and it’s slow as Christmas. I mean AOL speeds slow. If I download a similar size file from…

Best tool for genotype – phenotype correlation 0 Hello, I need to perform genotype – phenotype correlation analysis. I know PLINK could be used for such purpose, but with PLINK many file preparation steps need to be done before running the actual step. I have VEP annotated VCFs. Maybe other…

categorizing VEP annotations into consequences 1 Hello, I need to run downstream analysis where counts of functional and synonymous variants are needed. I have VCFs annotated with VEP. When annotating variants with VEP, in is not quite understandable, which outputs could be counted as synonymous and functional. It is, of…

Job Summary Primary accountability is to leverage the organization’s data assets exome sequencing data (>180,000 individuals) from MyCode Community Health Initiative to improve quality, efficiency and generate knowledge specifically in the field of bioinformatics within health research. Performs and supervises complex data extraction, transformation, visualization, and summarization to support Research…

VEP: “Given ref” field is empty when a ref. allele was in VCF input 0 Hi there, I’m running VEP using the following command: ref=”GRCh38.primary_assembly.genome.fa” vep=”/opt/vep_ensembl/ensembl-vep/vep” for ea in *Somatic.hc.vcf do $vep -i $ea -o vep/”$(echo $ea | sed s/.vcf//)”_VEP.txt –cache –dir_cache “/home/shared/vep_cache/” –assembly GRCh38 –merged –fasta $ref –hgvs –hgvsg…

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…

annotating vcf with variant type and variant effect, and most harmful effect 0 Hello, I have a VCF with ~6000 variants. The build is GRCh37. I want to annotate each variant with its type (substitution, deletion, inversion) and its effect (missense, silent, intergenic). If there are competing or multiple effects,…

VEP allele frequency from gnomAD genomes 1 Hi, Biostars community. According to VEP documentation, gnomAD genomes database could be used with –custom option. Example from VEP dosc: ./vep -i examples/homo_sapiens_GRCh38.vcf –cache –custom gnomad.genomes.r2.0.1.sites.GRCh38.noVEP.vcf.gz,gnomADg,vcf,exact,0,AF_AFR,AF_AMR,AF_ASJ,AF_EAS,AF_FIN,AF_NFE,AF_OTH But there is no gnomAD genomes file for all chromosomes on ensembl’s ftp source: ftp.ensembl.org/pub/data_files/homo_sapiens/GRCh38/variation_genotype/gnomad/r2.1/genomes/ Only data…

I have a vcf file with these column headers: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BS_25YES2E3 BS_G5B6AD28 BS_QCGPE1ZX A sample feature within that vcf file chr1 10450 . T C 27.94 VQSRTrancheSNP99.90to100.00+ AC=1;AF=0.167;AN=6;BaseQRankSum=-1.676e+00;ClippingRankSum=0.789;DP=102;ExcessHet=4.7712;FS=4.868;MLEAC=1;MLEAF=0.167;MQ=34.67;MQRankSum=-1.084e+00;PG=0,0,0;QD=1.55;ReadPosRankSum=-2.169e+00;SOR=0.707;VQSLOD=-1.050e+01;culprit=MQ;ANN=C|upstream_gene_variant|MODIFIER|**DDX11L1**|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1560|1||SNV|HGNC|HGNC:37102||||chr1:g.10450T>C,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1419|1||SNV|HGNC|HGNC:37102|YES|||chr1:g.10450T>C,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3954|-1||SNV|HGNC|HGNC:38034|YES|||chr1:g.10450T>C GT:AD:DP:FT:GQ:JL:JP:PL:PP 0/0:28,0:28:lowGQ:0:1:1:0,0,663:0,0,666 0/1:13,5:18:PASS:35:1:1:34,0,342:35,0,345 0/0:44,0:44:lowGQ:0:1:1:0,0,802:0,0,805 The portion in bold is what I want (DDX11L1). I…

adding allele frequencies to a vcf 1 Hi all, I have a vcf file generated from a few hundred samples. For each variant within the file, I would like to calculate the allele frequency of each allele and then add that information as a field into the ‘INFO’ field of…

VEP for cancer annotation using COSMIC 2 Dear all, I’m struggling in finding how to obtain information about COSMIC database after I annotate a vcf using VEP. The command that I used is: vep -i Mutect2_unfiltered_10643_vs_2434.vcf.gz -o Mutect2_unfiltered_10643_vs_2434_VEP.ann.vcf –assembly GRCh38 –species homo_sapiens –offline –cache –cache_version 99 –dir_cache /.vep –everything –filter_common…

VEP cache issues 1 Hello, need some help with VEP cache files. So, I downloaded cache file as written in this manual with www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#cache with curl -O ftp.ensembl.org/pub/release-102/variation/vep/homo_sapiens_vep_102_GRCh38.tar.gz I have file homo_sapiens_vep_102_GRCh38.tar.gz in my /.vep directory However, when running script, I got the error ——————– EXCEPTION ——————– MSG: ERROR: Cache…

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…

Ensembl vep. How to filter population frequency less than 1%? 0 Hi everyone, I have gotten many responses from the site even though I never asked a question, this is my first query. I am working with ensemble vep to annotate and filter a vcf file. With this script I…

How do I get GO term annotations using VEP? 1 I’m running VEP version 85 in offline mode, but I wasn’t asked to download any database for GO. I’m using the GO.pm plugin in my command-line, but the GO column is completely empty. The Clinvar column is not empty, and…

Vep : MNP phased genotype 0 Hello all, I would like to know what is the best way to annotate a vcf taking into account the mnp. I specify that it is about a vcf with phased genotype. For annotations i used ensembl vep. I saw that there is in…

Job details Job type full-time Full job description Job summary Primary accountability is to leverage the organization’s data assets exome sequencing data (>180,000 individuals) from mycode community health initiative to improve quality, efficiency and generate knowledge specifically in the field of bioinformatics within health researchPerforms and supervises complex data extraction,…

VEP: MSG: ERROR: Cannot use format vcf without Bio::DB::HTS::Tabix module installed 0 Hello everybody, I want to annotate a VCF file with vep (v. 104). I installed VEP and everything works fine. However, when using the –custom flag and a gnomAD.vcf file to annotate allele frequencies, I get the following…

Ensembl phylogenetic context 0 Hi, I was wondering if there is a way to download or generate 24 primates EPO-Extended alignments for a set of SNPs using Ensembl VEP. I can download it from the phylogenetic context section in Ensembl for a given SNP, but was wondering how to do…

    This package is for version 3.0 of Bioconductor; for the stable, up-to-date release version, see ensemblVEP. R Interface to Ensembl Variant Effect Predictor Bioconductor version: 3.0 Query the Ensembl Variant Effect Predictor via the perl API Author: Valerie Obenchain <vobencha at fhcrc.org>, Maintainer: Valerie Obenchain <vobencha at fhcrc.org>…

How to best predict effect for each variant and count specific effect found in each individual using variant effect predictor? 0 I have multiple .vcf files for individuals (also have merged.vcf with all indivs.). I would like to predict each variants effect and then count variants with, e.g. IMPACT=HIGH. Is…

Issues installing vep 0 I am having issues with installing ensembl’s vep on the HPC. It requires perl dependencies which I have successfully installed most of via anaconda. However I get the following error message when trying to run perl INSTALL.pl: Can’t locate Module/Build.pm in @INC (you may need to…

Job Title Bioinformatics Analyst II – Remote Location Work from Home Job Category Information Technology Support Services Schedule Days Work Type Full time Department Research Informatics Department Date posted 09/22/2021 Job ID R-15599 Job Summary Primary accountability is to leverage the organization’s…

Alamut batch vs free annotation tools like VEP 1 Hello all, we are considering purchasing an alamut batch license for variant annotation. I would like to have your opinion knowing that it is very expensive, I wonder what it really brings compared to VEP (with the use of plugin to…

Ensembl vep singularity 0 Hello all, I would like to use variant effect prédictor on an hpc cluster. For that i use singularity with the docker image of vep : singularity pull –name vep.sif But i have a problem to use one plugin because a perl module is missing….

Disease Causing Mutations Databases or database for predicting the functional consiquence of the mutation 1 I would like to analyze the functional consequence of the mutation in the protein-coding region of the human genome like in TP53 or EGFR etc. I tried Annovar, VEP, SIFT, polyphen, etc but as far…

Hi, I have installed VEP for offline use and I am trying to download the data for the gnomADc plugin. The instructions from VEP are as follows; genomes=”storage.googleapis.com/gnomad-public/release/3.0/coverage/genomes” genome_coverage_tsv=”gnomad.genomes.r3.0.coverage.summary.tsv.bgz” wget “${genomes}/${genome_coverage_tsv}” zcat “${genome_coverage_tsv}” | sed -e ‘1s/^locus/#chromtpos/; s/:/t/’ | bgzip > gnomADc.gz tabix -s 1 -b 2 -e 2 gnomADc.gz…

Ensembl VEP Plugin not working 0 Hi all… I’m using SubsetVCF plugin to extract some fields from my VCF file when using VEP annotator. I’ve noticed that using VCFv4.1, the plugin works fine but not with VCFv4.2. Are there any limitations to the VCF version that impacts the plugin? Does…

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,…

Job Summary Primary accountability is to leverage the organization’s data assets exome sequencing data (>180,000 individuals) from MyCode Community Health Initiative to improve quality, efficiency and generate knowledge specifically in the field of bioinformatics within health research. Performs and supervises complex data extraction, transformation, visualization, and summarization to support Research…

Vcf file sorting 1 I got vcf file from my instructor. It is VEP annoted with over 50 options separated by ||. I noticed that the vcf is not arrange to appropriate columns so I decided to sort it. I used this code to sort my vcf file according position:…

VEP plugin uses 0 It is a small question, I downloaded all plugins and wrote in the input script to get plugin experimental functionalities (I am using merged cache Ref_Seq & Ensembl both). # make a file with a single variant using bash echo “17 43071077 43071077 T/C + variant_1″…

Ensembl VEP Docker: cannot write to FASTA lockfile 0 Hello, I am trying to use the Ensembl VEP tool to annotate a database after liftover. For ease of use (or so I thought) I followed all the necessary steps decribed in the official documentation. I want to use local cache…

Interpreting dbNSFP prediction scores 1 How should I interpret for example, SIFT score: SIFT_pred = T;T;T;T;D;T SIFT_score = 0.138;0.138;0.138;0.138;0.042;0.157 From dbNSFP documentation, I understand the meaning of D and T D: Deleterious (sift<=0.05); T: tolerated (sift>0.05) My question is: Why there are multiple values of both pred and score in…

VEP output is only protein_coding 1 Hello, I am supposed to extract both protein coding and synonymous variants from VCFs that were given to me. Only variant consequence i find here is “Protein_coding”, but no strings as “synonymous” are present there. Is that some error with VEP? Thank you! VEP…

Bio-DB-HTS installation and ensembl-vep 0 I want to use ensembl-vep with custom annotation. In order to use gff file I need to have library Bio-DB-HTS installed. I downloaded Bio-DB-HTS and used Build.PL with no errors. When I try to install ensembl-vep it still gives an error asking for Bio-DB-HTS library….

Hello everyone, I am trying to run predixcan software. But its showing error as segmentation fault implying that there is something wrong with my vcf files. I am sharing the header of vcf file. ##fileformat=VCFv4.1 ##INFO=<ID=LDAF,Number=1,Type=Float,Description=”MLE Allele Frequency Accounting for LD”> ##INFO=<ID=AVGPOST,Number=1,Type=Float,Description=”Average posterior probability from MaCH/Thunder”> ##INFO=<ID=RSQ,Number=1,Type=Float,Description=”Genotype imputation quality from…

install ensembl-vep 0 Hello, I want to install ensembl-vep in my Ubuntu 18.04.2. I have already installed LWP::Simple. What can I do in the next step? Thanks in advance for great help! Best, Yue Inspiron-3670:~$ perl -MCPAN -e’install “LWP::Simple”‘ Reading ‘/home/jing/.cpan/Metadata’ Database was generated on Sat, 07 Aug 2021 06:55:53…