Question: Hg19 x GrCh38
0
gravatar for paulo
2.5 years ago by
paulo0
paulo0 wrote:

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

alignment snp next-gen assembly • 828 views
ADD COMMENTlink modified 18 days ago by Biostar ♦♦ 20 • written 2.5 years ago by paulo0

"PGX" ? "the allele *2" ?

ADD REPLYlink written 2.5 years ago by Pierre Lindenbaum122k

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

ADD REPLYlink written 2.5 years ago by paulo0

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?

ADD REPLYlink written 2.5 years ago by paulo0
1

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.

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by genomax70k

Ok. So I will try to find out. Tx

ADD REPLYlink written 2.5 years ago by paulo0

Either edit your original question or use ADD REPLY/ADD COMMENT when providing additional information/responding to existing posts to keep threads logically organized.

ADD REPLYlink written 2.5 years ago by genomax70k
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