How to annotate variants against hs37d5?
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6 months ago
vinayjrao ▴ 200


I am analyzing some data obtained from the EGA. I have successfully called the variants, but I am facing an issue while trying to annotate these using ANNOVAR, since ANNOVAR does not seem to support the genome version hs37d5. I read another post saying that Ensembl VEP can do do this, but upon trying the online version, I could not find the genome version of interest.

As far as I understand, hs37d5 is a more accurate version of hg19 (used for variant calling). So is it acceptable to use hg19 to annotate my variants in this case?

Thanks in advance

SNP annotation • 171 views

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