Hg19 x GrCh38
Hi guys we are using NGS for some PGX and we are facing a problem because our gene panel is based on Hg19, but for ex the CYP2D6 gene in this ref is the allele *2. When we use our vcf file many of the snps that are *2 are lost and we cant use the vcf file for genotyping so we must do it manually. The point is I can use my FASTQ (most based on Hg19) and align it with the GrCh38 once in this ref the CYP2D6 allele is *1? Tx
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"PGX" ? "the allele *2" ?
Pharmacogenomics. Allele 1 = CYP2D61 = Its called the reference or the normal allele for CYP2D6 drug metabolizer enzyme and the *2 allele is a polymorphism in this enzyme. Sorry
But my point is I could align FASTQ files (based on Hg19/Illumina) with the GRCH38? I will get the right chr positions of my snps?
Either edit your original question or use
ADD REPLY/ADD COMMENTwhen providing additional information/responding to existing posts to keep threads logically organized.So no matter what build you align to you want the answer to be projected on hg19?
Fastq files are plain sequence and are not based on any particular genome build.
Ok. So I will try to find out. Tx