RSID for multiple alternative variants present in a single line

Question

[ognjen011]

How does assigning RSID (dbsnp IDs) work when there are multiple variants at the same line? For example, if the genotype is 1/2, and of of these variants have a distinct RSID, would they both be assigned, separated by comma? And what about multi-sample VCFs, is the situation the same (e.g. 0/1 and 0/2)? Are there any limitations or recommendations on this?

[ognjen011]

Thanks for your reply, I didn't expect that but I see examples of it when I look through dbSNP. Does that mean a variant in dbSNP can be uniquely identified by {chr:pos_ref}? What about indels? Are they all bundled together as long as the position is the same or is this more complex?

[finswimmer]

Hello again,

please use the ADD REPLY button below a post you like to comment to. I moved your post to a comment now, but as you see this is not perfect.

Unfortunately rsIDs are not that unique as one would think. What you can take for sure is that an ID points to CHROM and POS. But you don't know what changes are behind such a number. AFAIK an rsID is always of the same type (SNV or INDEL). In case of INDEL I guess their can be of different length and still have the same rsID. In case of SNV the ALT can also have multiple values and the rsID is still the same.

Especially for INDELs it is possible that you have multiple IDs for the same variant, because this kind of variant can be described often in many ways.

fin swimmer

Answer 1

[finswimmer]

Hello ognjen011 ,

the ID column doesn't differ between multiple ALT values. This is why you cannot definitly say to which of the multiple ALT values an ID belongs. As long as the ALT values are of the same length, there is a good chance that the ID belongs to both, as (most of the time) all variants that map to the same position gets the same rsID.

fin swimmer

[ognjen011]

Thanks for the reply! Can you answer the above question in the comment as well?