SNP IDs
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3 months ago
kl ▴ 10

Dear all,

I have SNP IDS like these, where the last two columns denote the alleles. I would appreciate any suggestions of how to rename them. I am confused as to why it has a T-C alleles but then in the actual allele columns it has 0 and A?

CHR RSID
23  X:77378693-T-C 0 78123196 0 A
23. X:22112123-T-C 0 22094005 0 A

For other IDs, it the T-A corresponds to the allele codes. I am not sure if I should take the allele codes as they are (e.g., 0 and the other allele) or whether I need to look at the rsid column to deduce it but it doesn't

23. X:22112198-T-A 0 22094080 A T

Thanks

SNP • 705 views
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you joined this site 5 years ago but validated no answer...

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Give us a lot more context - where did you get these IDs from, for example. We cannot help you with just the information you've given us here.

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direct genotypes from the GSA-24v2-0, processed with plink 1.9.

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Is that your definition of "a lot more context"?

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I don't understand how much more context you need? Maybe if you can clarify please...I also don't appreciate sarcasm in a learning environment.

These are direct genotypes in a .bim file processed with plink 1.9 and genotyped using the array mentioned above.

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I apologize for the sarcasm. You're right, it does not belong in this environment and I crossed a line.

To investigate this further, I looked into plink1.9's bim format and I have a question. Was a liftover operation done at any point? Why are the coordinates in the ID column and the base-pair coordinate column different?

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I appreciate the apology.

As far as I know, no lift over has been performed. I have received this data from an institution. They were qc'ed based on allele freq, heterozygosity, missingness etc. The only check that was not done that I will do is a sex check but yes, I am not sure what is going on with chromosome 23 as some of the SNP names have two names alleles but the actual alleles in the columns are different.

23 X:106884169-T-C 104.570000 107640939 0 A

23 X:106884166-A-G 104.570000 107640936 0 A

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