Variant Effect Predictor | Sequencing.com

Variant Effect Predictor

Determine the effect of genetic variants

The Variant Effect Predictor app provides information about the effect of genetic variants on genes, regulatory regions, transcripts and protein sequences.

Free

Frequently Asked Questions

 

1) I used this app. How can I view the results?

This app currently generates a compressed vcf file (vcf.gz). To view the results, the file must be downloaded and opened on your computer.

Good news: We're already working on a better solution! In July 2017 we'll be releasing an update to this app that will allow you to view and search your results online without the need to download any files.

To view the contents of the vcf.gz file:

1) Download the file

2) Decompress the file. This can be accomplished by double-clicking on the file once it is downloaded to your computer.

  • Macs include decompression software for .gz files so the file should automatically start to decompress.
  • If you are using Windows and you don't have a program that decompresses .gz files, try WinZip.

3) View the file by opening it with either TextEditor or Excel. TextEditor is preferred as Excel may take a while to open the file.

  • Alternatively, you can change the extension by renaming the file and replace .vcf with .txt. After changing the extension, double click on the file and it should open in your computer's default viewer for txt files.

 

2) Are there any other similar apps?

Yes, there are two similar apps: Genome Overview and EvE Free

Genome Overview

Instructions for Genome Overview

1. Add Genome Overview to your account and then start the app (it's free)

2. Select your genetic data file

3. Click Submit

Once the Genome Overview app finishes processing your file, you'll receive an email with a link to the results. The results will include information about your genetic data as well as a searchable on-screen table called 'Details By Gene'. This table provides information that is similar to the information generated by the Variant Effect Predictor app.

 

EvE Free

Instructions for EvE Free

1) Add the EvE Free app to your account and then start the app

2) Select your genetic data file

3) For 'Select Target Format' choose "annotated vcf"

4) For 'Select Interpretation' choose "Both ClinVar Report & ClinVar Annotation"

5) Do not modify 'Select Reference Genome'. Leave it as the default "Autodetect"

6) Click Submit

Once Eve Free finishes processing your file, you'll receive an email with a link to the results. The results will include a searchable on-screen table that provides information about the impact of variants found within your genetic data file.

McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F. (2010) Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26(16):2069-70 doi:10.1093/bioinformatics/btq330