For microarray SNP data, I have a file containing the positions of all the SNPs. These SNPs originally came from Affy 6.0 chips but have been imputated since then. Thus, I have data on about 4.5 million SNPs and their positions... which is much more than the Affy 6.0 chips account for.
Looking at the position, it seems like the position stem from GRCh37 (hg19) instead of the more recent GRCh38 (hg38). By following Alex Reynolds advice here (how to find SNP positions (for non-bioinformaticians)) I was able to download the update SNP positions. Updating the SNP positions based on the rs# should be fairly straightforward using R.
The problem is, my data contains INDELs (e.g. chr1:730049:I at position 730049) and I am not really sure how to handle those positions. As these aren't coded with a rs#, I am a bit perplex about what to do with them.
Any advice would be appreciated!