The CYP2D6 VCF TRANSLATOR v2.0

The CYP2D6 variant call format (VCF) Translator v2.0 converts CYP2D6 sequence variants from human genome assembly GRCh37/hg19 coordinates to the M33388.1 and AY545216.1 GenBank reference sequence coordinates, which are commonly used for CYP2D6 star (*) allele conversion.

Key features:

  • The input is a standard VCF file (.vcf) with a file head and 10 columns (#CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, SAMPLE) limited to the full gene CYP2D6 coordinates from human genome reference hg19 (chr22:42522071-42528563).
  • The M33388.1 and AY545216.1 GenBank reference sequences have been modified to include the CYP2D6 nucleotide corrections indicated by the Human Cytochrome P450 (CYP) Allele Nomenclature Database.
  • Corrects for the CYP2D6*2 haplotype variants present in the hg19 human genome reference build (e.g., intron 1 conversion, 1661G>C, 2850C>T, 4180G>C, etc.).
  • Converts variants to their reverse complement as the CYP2D6 gene is encoded on the negative strand.
  • Coordinates and variant annotation can be downloaded as a tab delimited .txt file.

Updates in v2.0 (7/28/2017):

  • Multi-sample processing.
  • Updated CYP2D6 variant translation table.
  • VCF genotype fields denoted as ./. or “” are labeled as “Invalid Input” in the Results.

Select file to upload:


  

Instructions


  1. Click ‘Choose File’ to identify and select a local VCF file (.vcf).
  2. Click ‘Run’.
  3. Click ‘Open Result in New Tab’ to view the results onscreen or select ‘Download Result’ to download the .txt results file to a local drive.

Notes:

  • The #CHROM, POS, and SAMPLE columns of a VCF file are essential to run the CYP2D6 VCF Translator.
  • The input range of the POS field is limited to the CYP2D6 full gene and flanking region coordinates from human genome reference GRCh37/hg19 (chr22:42522071-42528563).
  • The CYP2D6 gene sequence of the hg19 genome reference build contains many common CYP2D6*2 variants. These variants will be homozygous reference in a VCF (and therefore not called) if they are actually homozygous for the minor allele in a sequenced sample. These variants could also be absent from a VCF file if they are outside of your sequenced region. Therefore, all CYP2D6*2 variants not called in a VCF are annotated in the output file as ‘Mutant or Not Sequenced’.

Terms of usage


  1. The CYP2D6 VCF Translator is available for use under the Attribution-NonCommercial 3.0 United States license. Any use not permitted by this license is expressly forbidden. If you wish to use this program for commercial or other purposes, please contact Dr. Stuart A. Scott here.
  2. The CYP2D6 VCF Translator is not a validated clinical device and, therefore, is intended for research use only. We do not provide any legal liability or responsibility for the completeness, accuracy, or correctness of this program.
  3. If users encounter any errors or bugs with the CYP2D6 VCF Translator, please contact us through the contact link and provide a brief description of the problem with an example dataset.
  4. User data uploaded to the CYP2D6 VCF Translator is not stored on any server; however, usage data will be collected to monitor the performance of the software on these datasets and to improve the usability and accuracy of this service.
  5. Please acknowledge the CYP2D6 VCF Translator by citing the reference for this online tool if used for your study.

Example


An example VCF is here.

Citation


Please cite the following reference as needed:
 Qiao W, Wang J, Pullman BS, Chen R, Yang Y, Scott SA. The CYP2D6 VCF translator. Pharmacogenomics J. 2017;17:301-303. [Epub 2016 Mar 15.]

Contact


Please send questions or comments here.