Tag: VEP

variant – Where should you put you cache for ensembl-vep using conda

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…

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linux – How to fix Perl from anaconda not installing bioperl? Bailing out the installation for BioPerl

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…

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Fail to install Ensembl VEP

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…

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VEP issue: ERROR: Cache assembly version (GRCh37) and database or selected assembly version (GRCh38) do not match

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…

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Installing Bio::DB::Big::File on Ubuntu (Building and testing…)

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…

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Failed to instantiate plugin dbNSFP in VEP

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…

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installation – Conda fails to install VEP

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…

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Conda failing to install VEP

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…

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Failing to install VEP dependencies

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…

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how do you get an IN-FRAME deletion stop gain variant?

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…

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Including tbi file along with VCF when running VEP on remote dataset (GnomadV3)

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…

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.vcf to.csv conversion

.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…

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Getting an error regarding the reference length and coordinates when using Ensembl-vep

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…

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Running a Linux command for “Ubuntu on Windows” with WSL from a python script

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…

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combine the same variant between the samples in the same line (question)

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…

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Error when trying to use Ensembl virtual machine

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…

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Annotating and prioritising genomic variants using the Ensembl Variant Effect Predictor – a tutorial

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…

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vcf – Ensembl Variant Effect Predictor (VEP) issue during execution

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

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Using VEP to get gnomAD frequencies

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…

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Ensembl FTP Mirror in USA? Slow Downloads

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…

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Best tool for genotype – phenotype correlation

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…

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categorizing VEP annotations into consequences

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…

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Bioinformatics Analyst II – Remote at Geisinger Health System

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…

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“Given ref” field is empty when a ref. allele was in VCF input

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…

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How to annotate SNVs in a BAC sequenced by NGS

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…

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annotating vcf with variant type and variant effect, and most harmful effect

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,…

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VEP allele frequency from gnomAD genomes

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…

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Sort a sub column within a column while keeping the feature (LINUX)

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…

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adding allele frequencies to a vcf

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…

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VEP for cancer annotation using COSMIC

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…

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VEP cache issues

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…

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Extract variant consequence count from gnomad and patient VCF file

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…

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Ensembl vep. How to filter population frequency less than 1%?

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…

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How do I get GO term annotations using VEP?

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…

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Vep : MNP phased genotype

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…

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Job vacancy in Global Worldwide: Bioinformatics Analyst II – Remote at Geisinger

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,…

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VEP: MSG: ERROR: Cannot use format vcf without Bio::DB::HTS::Tabix module installed

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…

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Ensembl phylogenetic context

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…

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Bioconductor – ensemblVEP

    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>…

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How to best predict effect for each variant and count specific effect found in each individual using variant effect predictor?

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…

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Issues installing vep

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…

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Bioinformatics Analyst II – Remote job in Danville at Geisinger

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…

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Alamut batch vs free annotation tools like VEP

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…

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Ensembl vep singularity

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….

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Disease Causing Mutations Databases or database for predicting the functional consiquence of the mutation

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…

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gnomADc plugin instructions not working for VEP

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…

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Ensembl VEP Plugin not working

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…

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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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Bioinformatics Analyst II in Danville, PA for Geisinger

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…

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Vcf file sorting

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:…

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VEP plugin uses

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″…

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cannot write to FASTA lockfile

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…

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Interpreting dbNSFP prediction scores

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…

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VEP output is only protein_coding

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…

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Bio-DB-HTS installation and ensembl-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….

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Inquiry related to vcf file and formatting

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…

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install ensembl-vep

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…

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