Question: Updating INDEL SNP positions
gravatar for JourneyToAbyss
18 months ago by
JourneyToAbyss90 wrote:

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!

snp • 341 views
ADD COMMENTlink modified 18 months ago by finswimmer13k • written 18 months ago by JourneyToAbyss90
gravatar for finswimmer
18 months ago by
finswimmer13k wrote:


converting positions from one assembly to another is called liftOver. Depending on the data format you can use one of these online tools to convert the positions:

fin swimmer

ADD COMMENTlink written 18 months ago by finswimmer13k
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