Difference between revisions of "Addon:DNASegmentMapGramplet"
m (GaryGriffin moved page Addon:DNAgramplet to Addon:DNASegmentMap: Initial name (DNAgramplet) too generic.)
Revision as of 20:28, 20 October 2020
This is a Third-party Addon.
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
The DNA Gramplet shows a DNA segment map as a graph.
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, shared length in cMs, SNP (optional).
3,56950055,64247327,10.9,1404Which means; Chromosome Number: 3, Start Segment: 56950055, End Segment: 64247327, shared length in cMs: 10.9, matching SNPs: 1404
- Valid entries for each are:
- The format of the Note is a comma separated list in the order:
- 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.
- Shared length in cMs
- The Genetic Distance otherwise known as the number of centiMorgans in the segment.
- optional field of the matching SNPs (Single Nucleotide Polymorphism) in the segment.
Getting the chromosome data
Sites like GEDmatch make this shared chromosome data available. There can be additional Associations between Person A and Person C et cetera as known.
- For each Chromosome the top portion is the Paternal side and the bottom portion is the Maternal side.
- The chromosome segment side (Paternal or Maternal) is determined from the Most Recent Common Ancestor. If there is no common ancestor, both sides are used.
- Hovering the cursor over a painted chromosome segment will show a tooltip with the name of the associated person, ID, length in cMs (centiMorgans) of the shared segment, and matching SNPs of the segment if provided.
- 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).
3,56950055,64247327,10.9,375 11,25878681,35508918,9.9,396 12,129481599,133491098,12.4,304 15,35444614,64710827,33.3,1212 1,48053426,68837810,24.6,3413 1,72956037,87857969,13.4,2035 3,69656569,74563488,9.0,974 6,6179882,15400114,18.5,1994
The second is for the DNA Association of Maude Garner (I0651).
1,30578594,38686908,11.2,334 1,236520701,249210707,29.7,685 3,14446545,24339734,12.3,458 3,128688499,140766208,11.4,447 4,76585823,114118650,33.7,1317 4,163973796,190915650,49.1,1422 6,4737179,9181572,10.3,279 6,39128976,49586285,15.8,510 6,150564916,156389148,10.2,415 7,18915133,37547290,25.8,1038 7,93557588,116296896,20.2,821 7,141636563,156148608,30.9,787 8,2808265,6919748,10.7,436 8,12568161,42652859,38.7,1556 8,49039681,71454529,20.3,742 8,71990280,99554231,21.9,917 9,78958599,122204804,55.7,2014 10,5608202,10769007,10.4,333 10,19365648,38434090,19.6,775 11,26722523,37020611,11.8,447 12,66412457,94422155,24.4,1035 13,19234747,23899627,8.7,270 13,74422984,91183468,14.2,506 14,23902753,33048583,15.5,392 14,88816167,106020366,37.8,947 15,23727655,27246462,8.2,229 16,22836249,32137965,12.6,413 16,46644903,54620503,11.7,360 17,13905,6613192,18.9,419 17,25567080,44187492,19.7,694 17,44790203,72115774,39.7,1223 18,18714991,47726830,27.9,1071 18,69454453,77894844,23.5,481 19,1993444,11174625,28.1,567 19,54545531,59087479,12.7,335 20,9879166,26225145,24.3,788 20,30221104,43975451,13.5,489 21,14670124,18743733,10.8,201
Create an Association of type DNA as described in the Association page to Person A. Add a Note with the DNA shared segment data. Set the Note private if you do not want the data printed in reports.
Save the Association.
Add more associations as known. Each would be associated to a different person and have a different Note. Since the Associations are drawn in order, it is generally better to have them in order of closest relative to furthest relative to avoid obscuring a distant relative (smaller segment) by a close relative (larger segment). Use the up-arrow and down-arrow to change the order of the Association.
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.
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.
- If the Chromosome Number is not in the range (1, 2, ..., 22, X) it is ignored.
- 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
- 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. Changing the order of Associations (using the up-arrow and down-arrow) to have the closer relatives before further relatives will fix this.
- Addon:SyncAssociation - For every Association, if there is not a reciprocal Association then it will be created. That is, where Person John Smith has a DNA Association (with an Association Note) to Person Jane Jones, then if Jane Jones does not have a corresponding DNA Association to John Smith, it will be created which shares the Note.
- Discourse forum discussion on the DNAgrample
- Roles, Relationships & Associations