Question: CYP2D6 Variant Calling
gravatar for twesigomwedavid
10 months ago by
twesigomwedavid0 wrote:

Hello, I would like to do variant calling on CYP2D6 using 1000 genomes data. What are the pros and cons of using GATK HaplotypeCaller on the CYP2D6 region?

Thank you.

variant calling • 222 views
ADD COMMENTlink written 10 months ago by twesigomwedavid0
gravatar for finswimmer
10 months ago by
finswimmer13k wrote:

Hello twesigomwedavid ,

in my opinion "pros and cons" for a particular variant caller isn't useful in the case of CYP2D6. The challenge in variant calling for this gene is, that there is a highly homolog gene (CYP2D7) next to it. That makes it difficult for the aligner to determine the origin of the reads. Furthermore it is well know, that there are recombination between the two genes.

I have no best strategy for calling variants in CYP2D6 from NGS for you. I did this with plain old sanger sequencing before, where I can amplify the CYP2D6 locus to make sure not to get the sequence of the CYP2D7 locus.

fin swimmer

ADD COMMENTlink written 10 months ago by finswimmer13k

Thank you fin swimmer

ADD REPLYlink written 9 days ago by twesigomwedavid0
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