A new feature in the inferred segments generator

Launched in late 2020, the inferred segments generator helps users calculate the segments they can infer from the DNA their close relatives share with others. This can be a confusing concept. I recently added a small additional feature to the tool that can help you infer segments from a grandparent. I’ll explain how this works below.

Recap

In the inferred segments generator you paste in two sets of segments:

1. The segments that you share with a match
2. The segments that a known relative shares with that same match

The goal is to capture just the segments that your relative shares with them, but which you don’t. You can then infer certain information about these segments based on the fact that you didn’t inherit them.

A simple example:

• If my brother shares segments with a second cousin, the grandson of our paternal grandfather’s sister, and I don’t share these segments…
• Then I know that in these positions I can’t have inherited DNA from my paternal grandfather (otherwise, I would have shared the same segments my brother has).
• I can therefore infer that I must have inherited DNA at these positions on the paternal copies of my chromosomes from my paternal grandmother.

For more background information on these concepts, you can read my original inferred mapping blog post and its follow-up.

The new tweak: infer segments from a grandparent

I’ve added a checkbox that is convenient in the scenario where you have the DNA of a grandparent. (For convenience, the explanation below is worded for the situation where it’s your grandparent, but this also works if you are yourself the grandparent!)

For example, if you have the segments you share with a maternal grandmother, but your maternal grandfather is not available to test, you can infer that any DNA you didn’t inherit from your mother’s mother must have come from your mother’s father. To infer these segments, you’d need to paste in

1. The segments you share with your maternal grandmother
2. The segments that your mother shares with her.  

But since this is a parent-child relationship, you already know that your mother inherited a complete set of chromosomes from her mother.  The new feature therefore allows you to do this with one click rather than having to compare them directly, by clicking populate this field with a full set of segments:

• Clicking this link will place the segments for every chromosome in the second box
• Then when you click ‘Generate Inferred Segments,’ the tool will output the segments that you can infer came from your mother’s father

You may notice that for chromosomes 13, 14, 15, 21 and 22, the start point is greater than 1. This is to allow for the unsampled and/or SNP-poor areas at the beginning of these chromosomes.

Tips for use

• When on Gedmatch, I find I need to check ‘prevent hard breaks’ to avoid gaps.
• If a parent has tested, use a phased kit to do the grandchild-grandparent comparison. This should lead to more accurate segment end points, although there will inevitably still be some fuzziness.
• Keep an eye on thresholds. There might be valid segments that are below the 7cM default.
• If you’re using Gedmatch, don’t forget to include X segments
• If you’re using MyHeritage, or if you’re a male working with segments from a paternal grandparent, you might need to remove the X chromosome segment within the second field if you use populate this field with a full set of segments to avoid the tool erroneously inferring a full X.

I hope this makes sense and is useful!

Contact info: @dnapainter / jonny@dnapainter.com