Timeline for Standardizing Variant IDs best practise
Current License: CC BY-SA 4.0
9 events
| when toggle format | what | by | license | comment | |
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| Oct 31, 2023 at 14:45 | comment | added | user27815 | yes, which is why I think some times chr:pos:effect:noneffect is often used, then that clears that up. But you still have the issue of population if the effect is differnt in differnt pops.. | |
| Oct 30, 2023 at 15:12 | comment | added | BigMistake | chr-pos-ref-alt is a good way to match variants, but may become problematic (without further tinkering) if the same variant has opposite effect sizes in different studies | |
| Oct 30, 2023 at 14:47 | comment | added | Ram RS | gnomAD uses chr-pos-ref-alt, not as an official ID but as a unique way to access web pages detailing each variant. That might be worth looking into. Example: gnomad.broadinstitute.org/variant/… | |
| Oct 30, 2023 at 14:28 | history | edited | BigMistake | CC BY-SA 4.0 |
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| Oct 30, 2023 at 14:27 | comment | added | BigMistake | @user27815 I see. I would try chr:pos:effect_allele in that case. Would that work? | |
| Oct 30, 2023 at 9:46 | comment | added | user27815 | Thanks for the response and your thoughts. I guess the thing is in the context of merging GWAS results for coloc and mr etc, chr:pos does not seem sufficeint. I can make sure everything in on the same build, but how do I know if an effect of a snp on say bmi in a japanese study can be matched to a study which finds an effect at the same position in a european study. I need to take into account ref/alt to effect non effect , direction.. | |
| Oct 29, 2023 at 17:12 | comment | added | BigMistake | @terdon Yes. I think chr:pos would be ideal/most simple, and OP would just have to be careful regarding builds | |
| Oct 29, 2023 at 17:05 | comment | added | terdon♦ | The vast majority of variants (remember that variants are effectively infinite since you can have any length of indel at any position) won't have rsIDs. Novel variants won't, by definition. So if the OP needs to work with arbitrary variants, rsIDs won't help. If not, rsIDs are indeed the best approach. | |
| Oct 29, 2023 at 16:30 | history | answered | BigMistake | CC BY-SA 4.0 |