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Background: I am looking for some advice on the use of SNP variants versus INDEL variants for determining Genetic Genealogy, specifically for determining accurately the "START" and "END" of shared DNA segments (shared between two DNA testers' results). The test data used is RAW DNA from direct to consumer DNA testing companies such as AncestryDNA and 23andMe.

Question: For the purpose of Genetic Genealogy, are the INDEL variants as useful as the SNP variants? Should the INDEL variants be ignored? Or, alternatively, do the INDEL variants hold a greater significance than the SNP variants?

I hope that using INDEL variants would increase the data in the comparison algorithm, thus increasing the certainty and resolution when determining each shared segment.

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InDels are just as informative, but are less reliable to call. Errors should be averaged out in this kind of analysis though (so long as they don't predominate).

Both SNPs and InDels are valid data points to consider when comparing triads, but identifying IBD segments will only ever be probabilistic.

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first of all there's no way to accurately determine the start/end position of shared DNA segments when using microarray data from DTC's like 23andMe and Ancestry.

INDEL's are indeed important when it comes to identify shared segments though I'm not sure how often the change over the course of several generations.

My mum's sister has an INDEL that both my mum and her brother didn't inherit, it will be inherited by her children (my 1st cousins).

Unfortunately the microarray from 23andMe doesn't give you any detailed information of than DI, II and II but not how long the deletion or insert is.

To determine such it requires to use WGS data.

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  • $\begingroup$ Welcome, for the answer to be valid you would need to share the putative indel location. The familial relationships could/should be anonymised but the biological information can't. $\endgroup$
    – M__ ♦
    Jan 12, 2020 at 3:40
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    $\begingroup$ Very informative. Thank you @a4xrbj1. I found that the length of the deletion can be read from the [link]ncbi.nlm.nih.gov/snp webpages, for example: [link]ncbi.nlm.nih.gov/snp/rs267607236. $\endgroup$
    – Stephen Dewar Millar
    Jan 14, 2020 at 19:09
  • $\begingroup$ @MichaelG. - I don't get your comment. This isn't a question about a specific INDEL, therefore it's a general answer. No idea why your asking for my aunt's specific INDEL at one chromosome and how that should help the OP. $\endgroup$
    – a4xrbj1
    Jan 15, 2020 at 7:08

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