# \#snpeff **URL:** https://help.galaxyproject.org/tag/snpeff/406.md [Latest](https://help.galaxyproject.org/latest.md) · [Categories](https://help.galaxyproject.org/categories.md) · [Tags](https://help.galaxyproject.org/tags.md) --- ## [Error in SnpEff version](https://help.galaxyproject.org/t/error-in-snpeff-version/17563)
**Author:** [@abhi\_g](https://help.galaxyproject.org/u/abhi_g)\ **Replies:** 4\ **Last updated:** [March 14, 2026, 3:39pm UTC](https://help.galaxyproject.org/t/error-in-snpeff-version/17563 "2026-03-14T15:39:06Z")
I used Snpeff on the output of VCFfilter tool at the version 5.2+galaxy1 and the result showed an error. The AI error analysis displayed that it may be due to the database file format changed between the 4.x and 5.x fa… --- ## [SnpEff eff (version 5.2)](https://help.galaxyproject.org/t/snpeff-eff-version-5-2/17288)
**Author:** [@xuanz01](https://help.galaxyproject.org/u/xuanz01)\ **Replies:** 7\ **Last updated:** [January 28, 2026, 5:26pm UTC](https://help.galaxyproject.org/t/snpeff-eff-version-5-2/17288 "2026-01-28T17:26:06Z")
I am using the examples provided by the MiModD tutorial called Mapping-by-sequencing: identification of a phenotype-causing mutation in a nematode genome. Using the updated version of snpeff (version 5.2) followed by MiM… --- ## [SnpEff eff - ERROR\_CHROMOSOME\_NOT\_FOUND](https://help.galaxyproject.org/t/snpeff-eff-error-chromosome-not-found/17323)
**Author:** [@Martin\_Larke](https://help.galaxyproject.org/u/Martin_Larke)\ **Replies:** 2\ **Last updated:** [January 19, 2026, 1:29pm UTC](https://help.galaxyproject.org/t/snpeff-eff-error-chromosome-not-found/17323 "2026-01-19T13:29:22Z")
Hello, I am trying to annotate a .vcf file of nucleotide changes in sample of Influenza B Virus genome vs the reference strain (B/Victoria/02/1987) with corresponding amino acid changes. I have built a SnpEff database … --- ## [Downloading SnpEff database into history: Create database instead!](https://help.galaxyproject.org/t/downloading-snpeff-database-into-history-create-database-instead/15963)
**Author:** [@boi\_incog](https://help.galaxyproject.org/u/boi_incog)\ **Replies:** 3\ **Last updated:** [July 18, 2025, 7:28pm UTC](https://help.galaxyproject.org/t/downloading-snpeff-database-into-history-create-database-instead/15963 "2025-07-18T19:28:48Z")
hi, tried adding hg19/GRCh37 to history via SnpEff downloads but didnt work. it said the file was empty. also tried uploading it via the “Upload data” section in which I set the file as “snpeffdb” format but still doesnt… --- ## [SnpEff errors while trying to run the tool](https://help.galaxyproject.org/t/snpeff-errors-while-trying-to-run-the-tool/3265)
**Author:** [@Pranav\_Menon](https://help.galaxyproject.org/u/Pranav_Menon)\ **Replies:** 3\ **Last updated:** [March 30, 2020, 4:16pm UTC](https://help.galaxyproject.org/t/snpeff-errors-while-trying-to-run-the-tool/3265 "2020-03-30T16:16:53Z")
Hi, I have been trying to run SnpEff in Galaxy, but have been facing a number of issues that I am not sure how to resolve. Background: I am analysis different strains of Mycobacterium tuberculosis. I have created a vcf … --- ## [Problems with snpEff databases](https://help.galaxyproject.org/t/problems-with-snpeff-databases/15719)
**Author:** [@angelbg](https://help.galaxyproject.org/u/angelbg)\ **Replies:** 2\ **Last updated:** [June 12, 2025, 8:44pm UTC](https://help.galaxyproject.org/t/problems-with-snpeff-databases/15719 "2025-06-12T20:44:13Z")
Hi, I’m trying to run snpEff eff on a FreeBayes vcf. Since it appears there are no ‘Locally installed snpEff databases’ (I get a ‘No options available’ in the field below), I tried to download a db with snpEff download.… --- ## [Job submission failed doing SnpEff eff](https://help.galaxyproject.org/t/job-submission-failed-doing-snpeff-eff/15447)
**Author:** [@bagoinj](https://help.galaxyproject.org/u/bagoinj)\ **Replies:** 4\ **Last updated:** [May 16, 2025, 7:01pm UTC](https://help.galaxyproject.org/t/job-submission-failed-doing-snpeff-eff/15447 "2025-05-16T19:01:58Z")
Hi I tried to submit a job and i got this error. Can someone help please? { “history\_id”: “54ccb97e3ead941e”, “tool\_id”: “toolshed.g2.bx.psu.edu/repos/iuc/snpeff/snpEff/5.2+galaxy0”, “tool\_version”: “5.2+galaxy0”, … --- ## [SNPEff eff job error](https://help.galaxyproject.org/t/snpeff-eff-job-error/15353)
**Author:** [@naila2025](https://help.galaxyproject.org/u/naila2025)\ **Replies:** 2\ **Last updated:** [May 1, 2025, 6:30pm UTC](https://help.galaxyproject.org/t/snpeff-eff-job-error/15353 "2025-05-01T18:30:36Z")
Hi, I am new to galaxy and doing a practice exome sequencing data analysis. When I am using “SNPEff eff” tool the job is giving the error (please see below). I have tried multiple times but its not working. Can anyone he… --- ## [Snpeff database run errors](https://help.galaxyproject.org/t/snpeff-database-run-errors/14929)
**Author:** [@gauthap](https://help.galaxyproject.org/u/gauthap)\ **Replies:** 3\ **Last updated:** [March 13, 2025, 5:47pm UTC](https://help.galaxyproject.org/t/snpeff-database-run-errors/14929 "2025-03-13T17:47:26Z")
Hello everyone, I’m trying to use Snpeff tool to annotate a vcf file containing variants called with FreeBayes on Bos taurus (cow). However, it appears that I cannot generate any proper output file. I have tried to cre… --- ## [SnpEff build: Create Vaccinium meridionale database](https://help.galaxyproject.org/t/snpeff-build-create-vaccinium-meridionale-database/14137)
**Author:** [@Ginna\_Patricia\_Velas](https://help.galaxyproject.org/u/Ginna_Patricia_Velas)\ **Replies:** 3\ **Last updated:** [December 10, 2024, 10:25pm UTC](https://help.galaxyproject.org/t/snpeff-build-create-vaccinium-meridionale-database/14137 "2024-12-10T22:25:01Z")
Hi, I am attempting to identify whether certain SNPs obtained through GBS are synonymous or non-synonymous mutations and to determine their effects on the sequences. To achieve this, I am trying to create a database for… --- ## [SnpEff database compatibility](https://help.galaxyproject.org/t/snpeff-database-compatibility/13923)
**Author:** [@Michael\_Thon](https://help.galaxyproject.org/u/Michael_Thon)\ **Replies:** 8\ **Last updated:** [November 20, 2024, 7:58am UTC](https://help.galaxyproject.org/t/snpeff-database-compatibility/13923 "2024-11-20T07:58:55Z")
I’m getting a warning from snpeff while configuring the analysis. First, I made a custom snpeff database which is in my history. Then, I configure the snpeff tool and select the database. When I click run, I get a war… --- ## [Snpeff eff error due to incompatible database version](https://help.galaxyproject.org/t/snpeff-eff-error-due-to-incompatible-database-version/13826)
**Author:** [@AM2023](https://help.galaxyproject.org/u/AM2023)\ **Replies:** 3\ **Last updated:** [November 5, 2024, 6:33pm UTC](https://help.galaxyproject.org/t/snpeff-eff-error-due-to-incompatible-database-version/13826 "2024-11-05T18:33:40Z")
I’ve created a database using SnpEff-build, this generates a version 5.2 database. However, when I try to annotate variants using SnpEff-eff and select the newly created database, the tool is unable to run and gives me t… --- ## [SnpEff build: Create Manihot esuclenta database](https://help.galaxyproject.org/t/snpeff-build-create-manihot-esuclenta-database/12302)
**Author:** [@Emili\_Ishikawa\_Garci](https://help.galaxyproject.org/u/Emili_Ishikawa_Garci)\ **Replies:** 3\ **Last updated:** [June 29, 2024, 8:28am UTC](https://help.galaxyproject.org/t/snpeff-build-create-manihot-esuclenta-database/12302 "2024-06-29T08:28:46Z")
Hi, I need to identify if some SNPs obtained through GBS are synonymous or non-synonymous mutations and what their effect is on the sequences. To do this, I am trying to create a database for Manihot esculenta V8.1, usi… --- ## [FreeBayes variant calling and Snpeff variant annotation](https://help.galaxyproject.org/t/freebayes-variant-calling-and-snpeff-variant-annotation/12406)
**Author:** [@Isa](https://help.galaxyproject.org/u/Isa)\ **Replies:** 18\ **Last updated:** [May 23, 2024, 9:26pm UTC](https://help.galaxyproject.org/t/freebayes-variant-calling-and-snpeff-variant-annotation/12406 "2024-05-23T21:26:27Z")
Hi, I am very new to Galaxy and bioinformatics overall (I have never had any education in it), however I am using Galaxy for my internship project, which involves analyzing NGS data from eight different yeast strains to… --- ## [Subject: Urgent Assistance Needed with SnpEff Custom Database Creation](https://help.galaxyproject.org/t/subject-urgent-assistance-needed-with-snpeff-custom-database-creation/11504)
**Author:** [@Muhammad\_Rizwan](https://help.galaxyproject.org/u/Muhammad_Rizwan)\ **Replies:** 2\ **Last updated:** [January 19, 2024, 7:11pm UTC](https://help.galaxyproject.org/t/subject-urgent-assistance-needed-with-snpeff-custom-database-creation/11504 "2024-01-19T19:11:05Z")
Subject: Urgent Assistance Needed with SnpEff Custom Database Creation Dear Galaxy Server Admin, I’m writing to seek your assistance with creating a custom SnpEff database for my organism, \[organism name\]. I’ve been wo… --- ## [Regarding SNP eff](https://help.galaxyproject.org/t/regarding-snp-eff/11480)
**Author:** [@Muhammad\_Rizwan](https://help.galaxyproject.org/u/Muhammad_Rizwan)\ **Replies:** 1\ **Last updated:** [January 16, 2024, 7:51pm UTC](https://help.galaxyproject.org/t/regarding-snp-eff/11480 "2024-01-16T19:51:48Z")
hello galaxy community, I require assistance with SNP Eff analysis for my Candida species, which isn’t on the pre-configured list. While I’ve attempted creating a custom database using GenBank GFF/GBFF/GTF formats, it’s… --- ## [Variant Calling from RNAseq](https://help.galaxyproject.org/t/variant-calling-from-rnaseq/11491)
**Author:** [@mitchellgc](https://help.galaxyproject.org/u/mitchellgc)\ **Replies:** 1\ **Last updated:** [January 16, 2024, 7:26pm UTC](https://help.galaxyproject.org/t/variant-calling-from-rnaseq/11491 "2024-01-16T19:26:10Z")
As mentioned, my question has to do with variant calling using RNAseq data. My workflow is basically: Trimmomatic → HISAT2 → FreeBayes → VCF filter → snpeff eff My question is about the results of snpeff (see below). Ho… --- ## [SnpSift Annotate](https://help.galaxyproject.org/t/snpsift-annotate/5868)
**Author:** [@AlBurl](https://help.galaxyproject.org/u/AlBurl)\ **Replies:** 0\ **Last updated:** [April 27, 2021, 3:09pm UTC](https://help.galaxyproject.org/t/snpsift-annotate/5868 "2021-04-27T15:09:35Z")
Dear all, I am receiving this error when trying to apply SnpSift Annotate to a hg38 VCF file, using dbSNP\_146\_hg38.vcf as reference downloaded from Galaxy shared data. Picked up \_JAVA\_OPTIONS: -Djava.io.tmpdir=/galaxy-… --- ## [SnpEff Chromosome Not Found Error](https://help.galaxyproject.org/t/snpeff-chromosome-not-found-error/6460)
**Author:** [@osman.merdan](https://help.galaxyproject.org/u/osman.merdan)\ **Replies:** 0\ **Last updated:** [August 4, 2021, 7:02am UTC](https://help.galaxyproject.org/t/snpeff-chromosome-not-found-error/6460 "2021-08-04T07:02:28Z")
Hi everyone, I am trying to get variants for a Candida glabrata isolate. I have already done mapping with Bowtie2 and variant calling with FreeBayes ( with the option for monoploid genome ). I couldn’t find and snpeff … --- ## [About INS annoation (snpEff)](https://help.galaxyproject.org/t/about-ins-annoation-snpeff/10605)
**Author:** [@Mume\_Clarence](https://help.galaxyproject.org/u/Mume_Clarence)\ **Replies:** 0\ **Last updated:** [August 10, 2023, 10:38am UTC](https://help.galaxyproject.org/t/about-ins-annoation-snpeff/10605 "2023-08-10T10:38:55Z")
I ran the INS annotation by using the delly results, and found most variants showed “.” on INFO column. Does that mean no annotated features? Thank you --- ## [TB-Profiler is not working anymore](https://help.galaxyproject.org/t/tb-profiler-is-not-working-anymore/10398)
**Author:** [@Darja\_Sadovska](https://help.galaxyproject.org/u/Darja_Sadovska)\ **Replies:** 1\ **Last updated:** [July 6, 2023, 11:29pm UTC](https://help.galaxyproject.org/t/tb-profiler-is-not-working-anymore/10398 "2023-07-06T23:29:16Z")
Hi there! Did not analyze my WGS data for a while, and now TB-Profiler tool is not working anymore. I have checked everything, and it still shows, that there is an error: File “/usr/local/lib/python3.9/site-packages/pat… --- ## [Tutorials, tools, and custom reference genomes](https://help.galaxyproject.org/t/tutorials-tools-and-custom-reference-genomes/10189)
**Author:** [@player\_777](https://help.galaxyproject.org/u/player_777)\ **Replies:** 1\ **Last updated:** [June 6, 2023, 12:00am UTC](https://help.galaxyproject.org/t/tutorials-tools-and-custom-reference-genomes/10189 "2023-06-06T00:00:17Z")
What Galaxy instance has Tuberculosis WGS new tools from the ToolShed and how to install them on the EU Instance? Need tools like: |Name↓|Synopsis|Type|Metadata Revisions|Owner| |galru|Long read spoligotyping for Myc… --- ## [SnpEff eff: annotate variants is producing errors](https://help.galaxyproject.org/t/snpeff-eff-annotate-variants-is-producing-errors/9771)
**Author:** [@Gavers\_Oppong](https://help.galaxyproject.org/u/Gavers_Oppong)\ **Replies:** 2\ **Last updated:** [April 1, 2023, 8:14am UTC](https://help.galaxyproject.org/t/snpeff-eff-annotate-variants-is-producing-errors/9771 "2023-04-01T08:14:58Z")
Hello, Please I am getting error using SnpEff since yesterday, I had results a day before using the same settings and data type. Please I want to know if there is something wrong somewhere thank you. Gavers --- ## [Errors urgent in variant filtering and insertsize](https://help.galaxyproject.org/t/errors-urgent-in-variant-filtering-and-insertsize/9376)
**Author:** [@Zachary\_Ramsay](https://help.galaxyproject.org/u/Zachary_Ramsay)\ **Replies:** 1\ **Last updated:** [March 10, 2023, 7:26pm UTC](https://help.galaxyproject.org/t/errors-urgent-in-variant-filtering-and-insertsize/9376 "2023-03-10T19:26:19Z")
First I need to select variants that are exonic and not in the 1000 genomes project. The 100G is coded in columns 11 to 16 as a “.” or “” used when its missing and whether its exonic or not in column 6. I uploaded a wANN… --- ## [Genom not found in SnpEff annotation](https://help.galaxyproject.org/t/genom-not-found-in-snpeff-annotation/9289)
**Author:** [@Sofi](https://help.galaxyproject.org/u/Sofi)\ **Replies:** 1\ **Last updated:** [January 13, 2023, 11:03pm UTC](https://help.galaxyproject.org/t/genom-not-found-in-snpeff-annotation/9289 "2023-01-13T23:03:47Z")
I create .vcf file and use reference by Galaxy hg38 (GRCh38.p2). I downloaded my file after SnpSift Annotate and trying use it for SnpEff annotation in cygwin64. I have error “GRCh38.p2 genom not found” because it’s not … --- ## [Filtering SnpEff output with SnpSift](https://help.galaxyproject.org/t/filtering-snpeff-output-with-snpsift/9242)
**Author:** [@abbi](https://help.galaxyproject.org/u/abbi)\ **Replies:** 2\ **Last updated:** [January 4, 2023, 7:18am UTC](https://help.galaxyproject.org/t/filtering-snpeff-output-with-snpsift/9242 "2023-01-04T07:18:27Z")
Hi, Please can I just ask how to filter SnpEff output for exonic variants only with SnpSift? I have tried by calling the initial SnpEff job with sequence ontology annotations. When I then try to filter as per the sequ… --- ## [Genome file missing in SNP calling session "From NCBI's Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis"](https://help.galaxyproject.org/t/genome-file-missing-in-snp-calling-session-from-ncbis-sequence-read-archive-sra-to-galaxy-sars-cov-2-variant-analysis/8932)
**Author:** [@wcq848677](https://help.galaxyproject.org/u/wcq848677)\ **Replies:** 1\ **Last updated:** [October 31, 2022, 9:17am UTC](https://help.galaxyproject.org/t/genome-file-missing-in-snp-calling-session-from-ncbis-sequence-read-archive-sra-to-galaxy-sars-cov-2-variant-analysis/8932 "2022-10-31T09:17:21Z")
HI Thanks for providing such an important training session ( From NCBI’s Sequence Read Archive (SRA) to Galaxy: SARS-CoV-2 variant analysis). I learned a lot from the Galaxy platform. When I processed the step ’ Annota… --- ## [Unable to select VCF with Gemini load? Tool form includes full input requirements](https://help.galaxyproject.org/t/unable-to-select-vcf-with-gemini-load-tool-form-includes-full-input-requirements/8207)
**Author:** [@Shuchi](https://help.galaxyproject.org/u/Shuchi)\ **Replies:** 1\ **Last updated:** [June 21, 2022, 2:10am UTC](https://help.galaxyproject.org/t/unable-to-select-vcf-with-gemini-load-tool-form-includes-full-input-requirements/8207 "2022-06-21T02:10:40Z")
Hi, I have generated the file using snpsift annotate (snpEff tool). This file is not recognised by Gemini load. Possibly, there is an issued in type of input files. What should be the input fie in the 2nd option? 1.Va… --- ## [unable to find SnpEff eff tool in Galaxy Australia](https://help.galaxyproject.org/t/unable-to-find-snpeff-eff-tool-in-galaxy-australia/8073)
**Author:** [@Thara\_Dharanidhar](https://help.galaxyproject.org/u/Thara_Dharanidhar)\ **Replies:** 1\ **Last updated:** [June 18, 2022, 6:21am UTC](https://help.galaxyproject.org/t/unable-to-find-snpeff-eff-tool-in-galaxy-australia/8073 "2022-06-18T06:21:23Z")
Hi, I am currently working on my project and is using the tutorial “Exome sequencing data analysis for diagnosing a genetic disease”. I could not find the tool called SnpEff eff and SnpEff Download. So where i can find t… --- ## [exome sequencing GEMINI load error](https://help.galaxyproject.org/t/exome-sequencing-gemini-load-error/8034)
**Author:** [@Thara\_Dharanidhar](https://help.galaxyproject.org/u/Thara_Dharanidhar)\ **Replies:** 6\ **Last updated:** [May 25, 2022, 6:28am UTC](https://help.galaxyproject.org/t/exome-sequencing-gemini-load-error/8034 "2022-05-25T06:28:42Z")
I am currently doing my project work on Exome sequencing and is using the following tutorial (Exome sequencing data analysis for diagnosing a genetic disease). I have an error in GEMINI load tool. It is showing that the … [Next page](https://help.galaxyproject.org/tag/snpeff/406.md?match_all_tags=true&page=1&tags%5B%5D=snpeff)