Hi all,
In the ROSMAP SNP Array unimputed genotype data ([data](https://www.synapse.org/#!Synapse:syn17008939)), I encountered a number of variants in the SNP_A and AFFX-SNP format. Could I please have some advice on converting these to rsid or hg19?
Here is my list of SNP_A and AFFX-SNP variant IDs: [Variants](https://docs.google.com/spreadsheets/d/1Vb0vmm3GE8K5YxnE4VqTK4_dpBj81oyWEx8R7goMDmM/edit?usp=sharing)
Thanks!
Created by wfli2 Hi @sieberts ,
Thank you for your answer to William Li (@wfli2 )'s question.
We are trying to re-run genotype imputation on our own using the latest reference panel to recover variants not present in the previous version of genotype imputation, including the one on the X chromosome.
We wanted to know if there was an easy way to retain the most genetic variants to have the maximum performance in genotype imputation.
With your clarification, we now understand that it is not easy to recover those variants. We agree that those variants are likely of low quality.
Thank you very much for your help, and have a great holiday weekend!
Best regards,
Yosuke
No particular reason, I just wanted to check if there was a straightforward way to not lose those variants. Thanks so much for your help! They typically don't have annotations because they don't map to subsequent genome builds after their initial development or are otherwise of low quality. There aren't that many of them. Is there a particular reason you want to try to rescue them? The last thing you can try is to see if you can track down their probe sequence and try to map that to your preferred genome build, but I suspect this won't be worth your time based on the number of SNPs in this category and the fact that they've fallen out of previous attempts to do this. Thanks so much for the quick response! I will lift over the ones that have annotations.
I noticed that a number of the SNP_A variants and one AFFX-SNP variant don't seem to be annotated at all (they're marked as chromosome number 0 and position 0). Do you have any suggestions in these cases for rescuing? Often these are proprietary SNPs that don't map to dbSNP. If you want to try to rescue them, you can try to lift them over to hg19 from their annotated location.
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