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.
- 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.