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. 2017 Jul;17(4):301-303.
doi: 10.1038/tpj.2016.14. Epub 2016 Mar 15.

The CYP2D6 VCF Translator

W Qiao  1 , J Wang  1   2 , B S Pullman  3 , R Chen  1   2 , Y Yang  1 , S A Scott  1
Affiliations

The CYP2D6 VCF Translator

W Qiao et al. Pharmacogenomics J. 2017 Jul.
No abstract available

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Conflict of interest statement

CONFLICT OF INTEREST

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
An overview of the CYP2D6 variant call format (VCF) Translator with (a) a screenshot of the online homepage (http://stuartscottlab.org/vcf) and (b) example input (.vcf) and output (.txt) files. Highlighted in red boxes are some of the key components of the input and output files of an example VCF using DNA from the NA12878 HapMap cell line with a CYP2D6*3/*4 diplotype sequenced through chr22:42522044–42527019 (hg19), or − 225 to 4752 using M33388.1 coordinates. Note the variants in the output file annotated as ‘Mutant or Not Sequenced’: − 1584C>G was not called in the VCF as it is outside of the sequenced region, and the common intronic 746C>G and downstream 4722T>G variants were not called in the VCF as they are found on both the *3 and *4 haplotypes, as well as in hg19. As such, these three variants were classified as ‘Mutant or Not Sequenced’ by the CYP2D6 VCF Translator (blue asterisk). Similarly, the original VCF shows homozygous variants for the CYP2D6 intron 1 conversion, 2850C>T, 3584G>A and 3790C>T; however, this is actually a reflection of those variants being present in hg19 and not in NA12878. As such, these variants were corrected to wild-type (WT) by the CYP2D6 VCF Translator (green asterisks).
See this image and copyright information in PMC

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