# Question about Annotating SNPs

**URL:** <https://discuss.hail.is/t/question-about-annotating-snps/3128>\
**Category:** Hail Query & hailctl\
**Created:** [February 20, 2023, 5:18pm UTC](https://discuss.hail.is/t/question-about-annotating-snps/3128 "2023-02-20T17:18:13Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![yixhe](https://avatars.discourse-cdn.com/v4/letter/y/ad7895/32.png) [@yixhe](https://discuss.hail.is/u/yixhe)\
**Post date:** [February 20, 2023, 5:18pm UTC](https://discuss.hail.is/t/question-about-annotating-snps/3128/1 "2023-02-20T17:18:13Z")

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Hi - I’m very new to using Hail so apologies if this has been asked before, but I am trying to annotate roughly 12 million variants with their RSIDs and have 2 questions:

1. I have columns for chrom, pos, ref, and alt alleles; however, some of the ref alleles are missing or have indels instead (e.g. ins:me:Alu). Is there a way to annotate just based on chrom and position only?
2. About half of the SNPs aren’t being annotated even know there is no missing info. for example 1:758085:T:C does not get annotated but exists on ncbi [https://www.ncbi.nlm.nih.gov/snp/rs537313150](https://www.ncbi.nlm.nih.gov/snp/rs537313150)?  
Thanks!