Addon:DNASegmentMapGramplet

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Revision as of 04:24, 15 October 2020 by Gioto (talk | contribs) (Create a DNA Association)
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Gramps-notes.png

Please use carefully on data that is backed up, and help make it better by reporting any comments or problems to the author, or issues to the bug tracker
Unless otherwise stated on this page, you can download this plugin by following these instructions.
Please note that some Addons have prerequisites that need to be installed before they can be used.
This Addon/Plugin system is controlled by the Plugin Manager

Example DNA Gramplet

The DNA Gramplet shows a DNA segment map as a graph.

Usage

You can install the DNA Gramplet on the bottombar of one of the people category list views.

Create a DNA Association

To specify shared DNA segments between 2 people,

  • Create an Association for one person (Person A) with another Person (Person B) of the type DNA.
  • Create a Note in the Association of Type: "Association Note" with the shared DNA segment data.
    • The format of the Note is a comma separated list in the order: Chromosome Number, Start Segment, End Segment, Flag for maternal/paternal side, shared length in cMs.
    • eg: 3,56950055,64247327,M,10.9 Which means; Chromosome Number: 3, Start Segment: 56950055, End Segment: 64247327, Flag for maternal/paternal side: M (for maternal side), shared length in cMs: 10.9
    • Valid entries for each are:
Chromosome Number
number between 1-22 or X
Start Segment
The starting number for the segment location.
End Segment
The endinging number for the segment location.
Flag for maternal/paternal side
refer to the following table:
Flag for maternal/paternal side Description
M Maternal side
P Paternal side
U Unknown side
Shared length in cMs
The Genetic Distance otherwise known as the number of centimorgans in the segment.


Sites like GEDmatch make this shared chromosome data available. There can be additional Associations between Person A and Person C et cetera as known.

Legend

  • For each Chromosome the top portion is the P (Paternal) side and the M (Maternal) side is the bottom portion.
  • If the chromosome segment side (Paternal or Maternal) is U (Unknown side), the segment will cover both the top and bottom portions of the chromosome and be 50% transparent.
  • Hovering the cursor over a known chromosome segment will show a pop up a tooltip with the name of the associated person and the length (in cMs (centimorgans)) of the shared segment.
  • The color code for each associated person in the DNA segment map is consistent but not user-specified. The first Association will always be the same color.

DNA Example data

To reproduce the illustration with the Example.gramps dataset, create two Associations of type DNA for Luther Robinson(I0656).

The first is DNA Association for Robert F. Garner (I1123).

3,56950055,64247327,M,10.9
9,23087926,31116823,M,10.2
9,74923489,107731789,M,40.0
11,25878681,35508918,M,9.9
12,129481599,133491098,M,12.4
15,35444614,64710827,M,33.3
1,48053426,68837810,M,24.6
1,72956037,87857969,M,13.4
3,69656569,74563488,M,9.0
6,6179882,15400114,M,18.5

The second is for the DNA Association of Maude Garner (I0651).

1,30578594,38686908,M,11.2
1,236520701,249210707,M,29.7
3,14446545,24339734,M,12.3
3,128688499,140766208,M,11.4
4,76585823,114118650,M,33.7
4,163973796,190915650,M,49.1
6,4737179,9181572,M,10.3
6,39128976,49586285,M,15.8
6,150564916,156389148,M,10.2
7,18915133,37547290,M,25.8
7,93557588,116296896,M,20.2
7,141636563,156148608,M,30.9
8,2808265,6919748,M,10.7
8,12568161,42652859,M,38.7
8,49039681,71454529,M,20.3
8,71990280,99554231,M,21.9
9,78958599,122204804,M,55.7
10,5608202,10769007,M,10.4
10,19365648,38434090,M,19.6
11,26722523,37020611,M,11.8
12,66412457,94422155,M,24.4
13,19234747,23899627,M,8.7
13,74422984,91183468,M,14.2
14,23902753,33048583,M,15.5
14,88816167,106020366,M,37.8
15,23727655,27246462,M,8.2
16,22836249,32137965,M,12.6
16,46644903,54620503,M,11.7
17,13905,6613192,M,18.9
17,25567080,44187492,M,19.7
17,44790203,72115774,M,39.7
18,18714991,47726830,M,27.9
18,69454453,77894844,M,23.5
19,1993444,11174625,M,28.1
19,54545531,59087479,M,12.7
20,9879166,26225145,M,24.3
20,30221104,43975451,M,13.5
21,14670124,18743733,M,10.8

Example

Addon-DNA-Note-Example.png

Create an Association of type DNA as described in the Association page to Person A. Add a Note with the DNA shared segment data.


Addon-DNA-Association-Example.png

Save the Association.

Addon-DNA-Associations-Example.png

Add more associations as known. Each would be associated to a different person and have a different Note.

Addon-DNA-SegmentMap.png

Add the DNA gramplet to the Person view. Select the DNA tab. The segment map will be color coded by associated person. For each Chromosome the top portion is the P (Paternal) side and the M (Maternal) side is the bottom portion. If the chromosome segment side (Paternal or Maternal) is unknown, the segment will cover both the top and bottom portions of the chromosome and be 50% transparent.

Addon-DNA-SegmentMap-with-Tooltip.jpg

Hovering the cursor over a known segment will pop up the name of the associated person and the length (in cMs) of the shared segment.

Issues

  • If the Chromosome Number is not in the range (1, 2, ..., 22, X) it is ignored.
  • If there is a Most Recent Common Ancestor (MRCA), that relationship is used instead of the maternal/paternal flag. If the MRCA is thru the maternal side, then M is used independent of what is in the data file. If there are multiple paths to a common ancestor, the closest found is used.
  • To create a segment map for Person A, you need to add associations to Person A. There is no reciprocal relationship for Person B - that is, there is no segment map for Person B, only for Person A. You can execute the Addon:SyncAssociation addon to create any missing reciprocal relationships.
  • Color code for each associated person in the map is consistent but not user-specified. The first Association will always be the same color.
  • Help link goes to https://gramps-project.org/wiki/index.php?title=Gramps_5.1_Wiki_Manual_-_Gramplets#DNA
  • Source code - Unlisted Gramplet you need to manually download and install ( include_in_listing = False ) https://github.com/gramps-project/addons/raw/master/gramps51/download/DNA.addon.tgz
  • If there are overlapping segments within a maternal/paternal view of a chromosome, only the front (last drawn) will be pickable. If it is completely obscured, you will not be able to see the details of the hidden segment.

See also