Difference between revisions of "Talk:Addon:DNASegmentMapGramplet"

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(Future version of documentation - pending PR merge)
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[[User:Sam888|Sam]],
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{{languages|Addon:DNASegmentMapGramplet}}
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{{Third-party plugin}}
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[[File:Addon-DNA-SegmentMap-with-Tooltip2.png|thumb|450px|right|[[Gramps_{{man version}}_Wiki_Manual_-_Gramplets#The_split-screen_Sidebar_.26_Bottombar|Undocked]] {{man label|DNA Segment Map Gramplet}} with the HighContrast [[Addon:Themes|theme]]]]
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The {{man label|DNA Segment Map Gramplet}} shows a graph.
  
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Could you revert the filename and the Admin task of deleting the no-longer-needed new filename?
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=Usage=
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The purpose of this gramplet is to view DNA segment data for the active user and a set of associated users. Once the user has done an autosomal DNA test and uploaded their data to one of the vendors (GEDmatch or FamilyTreeDNA, for example), the vendor can calculate the shared DNA segments with others in their system. These list of people with their shared segments are input to this gramplet for visualization.
  
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The registration to the Gramplet uses the original Help URL of "[[Addon:DNASegmentMap|Addon:DNASegmentMap]]", not "[[Addon:DNASegmentMapGramplet|Addon:DNASegmentMapGramplet]]". This just creates extra server load with a redirect.
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Each person with shared segments will be a separate Association. The Notes in the Association should contain the shared segment info as calculated by the vendor.
  
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The "Gramplet" in the filename is redundant. If this page was going to be renamed, it should have be renamed to be more human readable and appear less "code-like" in the header ... with spaces between words.
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There are two views for this gramplet. The default view is all of the chromosomes with all of the segments, painted in the order of the Association. The second view is a detailed view of a single chromosome, with each associated person having a separate row. The user clicks on the chromosome label (y-axis) to switch to the detailed view and clicks on the background to return to the default view.
  
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(cur | prev) 20:36, 20 October 2020‎ Gioto (talk | contribs)‎ m . . (7,331 bytes) (0)‎ . . (Gioto moved page Addon:DNASegmentMap to Addon:DNASegmentMapGramplet: keep gramplet in the name) (undo)
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You can install the {{man label|DNA Segment Map Gramplet}} on the bottombar of one of the people or relationship category list views.
  
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[[User:Bamaustin|Bamaustin]] ([[User talk:Bamaustin|talk]]) 18:34, 17 November 2020 (UTC)
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==Create a DNA Association==
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To specify shared DNA segments between 2 people,
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* Create an Association for one person (Person A) with another Person (Person B) of the type DNA.
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* Create a Note in the Association or attached to a Citation in the Association with the shared DNA segment data.
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** The format of the Note is a comma separated list or a tab separated list in the order: <code>[https://wikipedia.org/wiki/Chromosome#Human_chromosomes Chromosome Number], Start Segment, End Segment, shared length in [[Genealogy_Glossary#centimorgan|centiMorgans]] (cMs), [https://wikipedia.org/wiki/Single-nucleotide_polymorphism SNP] (optional), M or P or U (unknown) to override the Maternal Paternal chromosome as determined by the closest genetic connection in the tree (optional). </code>.
 +
** e.g.: <code>3,56950055,64247327,10.9,1404</code> Which means; Chromosome Number: 3, Start Segment: 56950055, End Segment: 64247327, shared length in cMs: 10.9, matching SNPs: 1404</code>
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** Valid entries for each are:
  
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---
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;Chromosome Number: number between 1-22 or X
  
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Michal Maňas had difficulties posting here. Posting on his behalf:
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;Start Segment: The starting number for the segment location.
  
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There is also undocumented feature, that the addon is using segment data also from associated citations. I was very surprised, when I found that, because it added segments I was not not expecting. This should be somewhat written to the documentation.
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;End Segment: The ending number for the segment location.
  
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He wonders if a Maternal/Paternal mask could be added.
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;Shared length in cMs: The Genetic Distance (otherwise known as the number of centiMorgans) in the segment.
  
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He also created a Centromere position indicator via a dna segment map"
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;SNP: optional field of the matching SNPs (Single Nucleotide Polymorphism) in the segment.
  
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;M/P flag: optional field to override the Maternal or Paternal or Unknown chromosome. Valid entries are M or P or U. Any other data is ignored
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{{-}}
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===Getting the chromosome data ===
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Sites like [https://www.gedmatch.com/login1.php GEDmatch] make this shared chromosome data available. Direct copy from the GEDmatch results page (with header and tab separators) will work. There can be additional Associations between Person A and Person C (et cetera) as known.
 +
 +
[https://dnapainter.com/help/matchdata DNApainter] provides a description of how to get the chromosome data from many of the common sites.
 +
 +
===Legend===
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[[File:Addon-DNA-SegmentMap-legend.png|thumb|338px|right|[ {{man label|Legend with rollover tooltip]]
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* For each Chromosome: the top portion is the Paternal side and the bottom portion is the Maternal side.
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* 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.
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* 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.
 +
 +
===Navigation===
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* The Legend on the right side lists each associated person who has a mapped segment. Hovering over the legend items will show a tooltip for possible action. Primary button click will change the active person. Secondary button click will open the Person Editor for the associated person.
 +
* Hovering over the Y-axis chromosome labels will show a tooltip for possible action. Primary button click will switch view to single chromosome of the label clicked. To return to full view, click on the background in the single chromosome view.
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* Hovering over a segment provides detail on the segments at that location. If there are multiple segments overlapping, all will have details.
 +
 +
===Configuration===
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The config file for this gramplet has the following options. Remove the comment (double semi-colon) and edit as needed. Changes are not reflected until the next time the gramps is started.
 +
 +
<pre>
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[map]
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;;chromosome-build=37
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;;legend-single-chromosome-y-offset=25
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;;legend-swatch-offset-y=0
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;;maternal-background=(0.833, 0.845, 0.92)
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;;paternal-background=(0.926, 0.825, 0.92)
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;;show_associate_id=1
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</pre>
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* Chromosome Build: choose the specific build for the chromosomes. Options are 36, 37, 38.
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* Legend Single Chromosome Y offset: Adjust the height of the legend for the single chromosome view. This may be needed if more than 12 people share the chromosome.
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* Legend Swatch Offset: Offset for the color swatch in the legend. Should be 5 for Windows systems. 0 works for Linux and Mac
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* Maternal Background Color: RGB values for the background of the Maternal Chromosome
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* Paternal Background Color: RGB values for the background of the Paternal Chromosome
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* Show Associate ID: To remove the ID on the legend and tooltip, set to 0. Otherwise leave as 1 to print the Associate ID.
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 +
 +
===DNA Example data===
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To reproduce the illustration with the [[Example.gramps]] dataset, create two records in the Associations tab in the Person Editor for Luther Robinson(I0656).
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 +
The first record is DNA type, adding an association with Robert F. Garner (I1123).<br />
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The Note under this association contains the following text:
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Chromosome,Start Location,End Location,Centimorgans,Matching SNPs,Name,Match Name
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3,56950055,64247327,10.9,375,Luther Robinson, Robert F. Garner
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11,25878681,35508918,9.9,396
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12,129481599,133491098,12.4,304
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15,35444614,64710827,33.3,1212
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1,48053426,68837810,24.6,3413
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1,72956037,87857969,13.4,2035
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3,69656569,74563488,9.0,974
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6,6179882,15400114,18.5,1994 
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The second record is also DNA type, adding an association with Maude Garner (I0651).<br />
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The Note under this association contains the following text:
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1,30578594,38686908,11.2,334
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1,236520701,249210707,29.7,685
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3,14446545,24339734,12.3,458
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3,128688499,140766208,11.4,447
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4,76585823,114118650,33.7,1317
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4,163973796,190915650,49.1,1422
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6,4737179,9181572,10.3,279
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6,39128976,49586285,15.8,510
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6,150564916,156389148,10.2,415
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7,18915133,37547290,25.8,1038
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7,93557588,116296896,20.2,821
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7,141636563,156148608,30.9,787
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8,2808265,6919748,10.7,436
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8,12568161,42652859,38.7,1556
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8,49039681,71454529,20.3,742
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8,71990280,99554231,21.9,917
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9,78958599,122204804,55.7,2014
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10,5608202,10769007,10.4,333
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10,19365648,38434090,19.6,775
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11,26722523,37020611,11.8,447
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12,66412457,94422155,24.4,1035
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13,19234747,23899627,8.7,270
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13,74422984,91183468,14.2,506
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14,23902753,33048583,15.5,392
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14,88816167,106020366,37.8,947
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15,23727655,27246462,8.2,229
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16,22836249,32137965,12.6,413
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16,46644903,54620503,11.7,360
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17,13905,6613192,18.9,419
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17,25567080,44187492,19.7,694
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17,44790203,72115774,39.7,1223
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18,18714991,47726830,27.9,1071
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18,69454453,77894844,23.5,481
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19,1993444,11174625,28.1,567
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19,54545531,59087479,12.7,335
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20,9879166,26225145,24.3,788
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20,30221104,43975451,13.5,489
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21,14670124,18743733,10.8,201
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{{man tip|DNA match row data must be in a specific CSV order|The data may include a header but the Gramplet does not require one. Headers are to make the rows more readable by humans. The rows do not need to be sequentially ordered by the chromosome identifier (1 to 22 and X).}}
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[[File:Addon-DNA-GEDmatch.png|thumb|600px|right]]
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Sample GEDmatch output (see screenshot) that can be cut and paste into the Note. The fields are the same - Chromosome, Start, End, cM, and SNPs. This can be cut/paste from the GEDmatch output directly into the Note for the Association. The header line will be ignored.
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{{-}}
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=== Example ===
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[[File:Addon-DNA-Note-Example.png|thumb|600px|right]]
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Create an Association of type DNA as described in the [[Gramps_{{man version}}_Wiki_Manual_-_Entering_and_editing_data:_detailed_-_part_1#Associations|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.
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{{-}}
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[[File:Addon-DNA-Association-Example.png|thumb|600px|right]]
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Save the Association.
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{{-}}
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[[File:Addon-DNA-Associations-Example.png|thumb|600px|right]]
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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.
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{{-}}
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[[File:Addon-DNA-SegmentMap2.png|thumb|600px|right]]
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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.
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{{-}}
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[[File:Addon-DNA-SegmentMap-with-Tooltip2.png|thumb|600px|right]]
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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.
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{{-}}
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[[File:Addon-DNA-SegmentMap-Single.png|thumb|600px|right]]
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Clicking on the Y-axis label for the 6th chromosome, a detailed view is shown. Click on the background to return to the complete view.
 +
{{-}}
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== Reference Info ==
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=== Untested Areas ===
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There are areas in the DNA test that are generally not tested as they are not reliable indicators of a match. If you want to visualize these areas, create a dummy person and add an association with the following DNA segments.
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 +
<pre>
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13,1,19020094,0,0
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14,1,19067948,0,0
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15,1,20004965,0,0
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21,1,9922017,0,0
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22,1,16055121,0,0
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</pre>
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=== Centromere Areas ===
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Machines have difficulties to read the area around the centromere. There are less SNPs to read, therefore there is higher probability of false positive matches. For example, if you  have a match exactly around the centromere, then it is most probably a false positive match. If you want to visualize these areas, create a dummy person and add an association with the following DNA segments.
  
 
<pre>
 
<pre>
Line 48: Line 196:
 
</pre>
 
</pre>
  
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and a list of not tested regions:
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= To Do =
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<pre>
 
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13,1,19020094,0,0
 
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14,1,19067948,0,0
 
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15,1,20004965,0,0
 
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21,1,9922017,0,0
 
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22,1,16055121,0,0
 
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</pre>
 
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---
 
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I am not sure I follow. The map is all of the DNA Associated people. I don't understand what is the undocumented feature. I will certainly add it once I understand what it is. Can you provide a sample with expected vs actual results?
 
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I don't understand the untested regions comment. I don't think any of the sources of the DNA data (GEDmatch, FTdna, ...) have regions which are untested. So where exactly did these untested regions come from? And do they apply to all of the associated DNA files (if you have 5 associated people, did all 5 have these same untested regions)? If so, then the simplest way would be to create a dummy person (name of UNTESTED, for instance) with the untested DNA info. That will paint that data. Or am I misunderstanding?
 
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The Maternal/Paternal is determined by the tree itself. I realize this is slightly different than DNApainter uses, because that tool does not also have an associate tree. Initially I coded this with a maternal/paternal flag required for each line (like DNApainter). The downside was each line of each file now had to be editted to add this flag assuming you are cut/paste from GEDmatch or similar. But the relationship of maternal/paternal was per-person, not per-segment. So lots of unnecessary editing . And consider that Gramps already knows the relationship, so why add it again.
 
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In the case where you do not know which side, I can see why you might want to add a M/P flag to the person (not each line). What would be expected if the tree says the connection was on the paternal side and the DNA data had the flag for maternal? I removed the flag for these reasons.
 
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---
 
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I think we are mixing up Chromosome Painting with Chromosome Browsing.
 
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TLDR: Chromosome Painting uses the active person and a vendor-specific reference ethnicity map, whereas Chromosome Browsing uses shared segments between the active person and associated person(s). This gramplet implements the latter.
 
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'''Chromosome Painting'''
 
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The new AncestryDNA [https://support.ancestry.co.uk/s/article/Chromosome-Painter Chromosome Painter] has ‘untested’ segments. As does the FTDNA [https://www.familytreedna.com/my/chromosome-painting/graph Chromosome Painter]. These tools use the members DNA and compares the Ethnicity mappings that they have collected and paints the segment map appropriately. The ‘secret sauce’ is this ethnicity reference table, which each vendor builds based on the samples they have processed. There are ‘blank’ or untested areas in it. All you get is the ethnic region on the segment map (not a persons name). This is useful for understanding where a particular segment geographically came from, in hopes to indirectly guess on which line it comes from. The maternal/paternal are both painted based on their individual lookup of the Ethnicity map. There is no ambiguity on maternal vs paternal sides, since each side is painted based on the Ethnicity map independently.
 
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Let me exaggerate a point to simplify. If John Doe has a mother who is 100% German and a father who is 100% Irish, the map would have all of the maternal segments one color for Germany and the paternal segments all a different color for Ireland. And there would be grey segments where untested.
 
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The ‘secret sauce’ is proprietary to the vendor, so this really cannot be implemented in Gramps.
 
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'''Chromosome Browsing'''
 
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This is not the same as Chromosome Browsing, which is what [https://dnapainter.com/tools/acps DNApainter] and this gramplet do. The idea for this tool it to compare the active person with shared segments (created by GEDmatch or FTdna or …) of associated people and paint the segments that match, identifying which person maps with the active person. There are no ‘untested’ in this analysis. If the associated person is maternally related (based on the tree), then the maternal chromosome is painted. Conversely if they are paternally related, the paternal chromosome is painted. If the person is not genetically (known) connected, then both are painted (but with transparency).
 
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Example: If John Doe is related to Mary Smith thru his mother, then the shared segments they have would be painted on the segment map on the maternal side. If they are related thru Marys father, Mary’s map would have the paternal segment painted. The more people associated, the more different colors on the map.
 
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If you hover over the shared segment on the map, it will tell you the shared length (in cM). This provides a hint on the genetic distance.
 
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The Shared cM Project has a lookup for relationship to cM range. The ranges overlap significantly for lower cM values. Given a cM value, there is a large range of relationships possible. For instance. for 75 cM , the table from DNApainter (by Jonny Per) is [https://dnapainter.com/tools/sharedcmv4 HERE]. This is more info than is practical to display, even if it were public domain.
 
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--[[User:GaryGriffin|GaryGriffin]] ([[User talk:GaryGriffin|talk]]) 16:12, 14 October 2022 (UTC)
 
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I created a bug report for all of the recent suggestions: https://gramps-project.org/bugs/view.php?id=12712
 
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Given Michal wanted to add a M/P flag for each line and George wanted a comment for each line:
 
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Proposal: the input format changes from the required fields: Chromosome Number, Start, Stop, cM, SNPs to add an optional 6th field. If the new field is "M" or "P", it will override the tree-determined side of the chromosome. Otherwise the field is considered a comment for the purposes of the tooltip.
 
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Should the override only occur if there is no genetic path between the people (and the tool would otherwise paint both M and P sides)? Or should it even override the genetic path that the tree calculates.
 
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Does anyone have the definitive list of untested segments so that I can grey them out?
 
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--[[User:GaryGriffin|GaryGriffin]] ([[User talk:GaryGriffin|talk]]) 22:43, 15 October 2022 (UTC)
 
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One more update: Michal comment states that there is an undocumented feature. I think this is documented as:
 
  
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'''Create a Note in the Association or attached to a Citation in the Association with the shared DNA segment data.'''
 
  
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I have a draft update that I can provide for testing. It addresses the following issues:
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= Issues =
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* Fix maternal/paternal calculation when there are shared parents. Currently it chooses maternal.
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* If the Chromosome Number is not in the range (1, 2, ..., 22, X) it is ignored.
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* Grey out the paternal X chromosome if the active person is male.
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* If there are multiple paths to a common ancestor, the closest found is used.
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* Add an optional field to the chromosome line. It has two possible uses:
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* 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.
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** M/P/U (maternal/paternal/unknown) flag to each chromosome line. This will produce potentially wrong info if you use SyncAssociations since the Note is shared. That is, the forced M/P/U flag persists on the reverse relationship.
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* Color code for each associated person in the map is consistent but not user-specified. The first Association will always be the same color.
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** If the field is any other string, it will be used as a comment field for the tooltip.  
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* If there are overlapping segments within a maternal/paternal view of a chromosome, only the front (last drawn) will be pickable. The tooltip will still provide the details of the hidden segments. Changing the order of Associations (using the up-arrow and down-arrow) to have the closer relatives before further relatives will fix this.
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* Add start and stop values to the tooltip.
 
  
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Please let me know if you want to test these changes.  
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= See also =
 +
* DNA Segment Map gramplet #550 (GitHub pre-release [https://github.com/gramps-project/addons-source/pull/550])
 +
* [[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.
 +
* [[Add Types to the SyncAssociation Gramplet]]
 +
* [https://gramps.discourse.group/t/updated-dna-gramplet-ready-for-review/807 Discourse forum discussion on the DNAgramplet]
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* [[Gramps_{{man version}}_Wiki_Manual_-_Entering_and_editing_data:_detailed_-_part_1#Associations|Introduction to Associations in Gramps]]
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* [[Roles, Relationships & Associations]]
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* [[Genetics]]
  
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--[[User:GaryGriffin|GaryGriffin]] ([[User talk:GaryGriffin|talk]]) 21:51, 16 October 2022 (UTC)
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[[Category:Plugins]]
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[[Category:Addons]]

Revision as of 18:59, 5 November 2022

Gramps-config-language.png Languages: 

English

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 addon 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.

Undocked DNA Segment Map Gramplet with the HighContrast theme

The DNA Segment Map Gramplet shows a graph.

Usage

The purpose of this gramplet is to view DNA segment data for the active user and a set of associated users. Once the user has done an autosomal DNA test and uploaded their data to one of the vendors (GEDmatch or FamilyTreeDNA, for example), the vendor can calculate the shared DNA segments with others in their system. These list of people with their shared segments are input to this gramplet for visualization.

Each person with shared segments will be a separate Association. The Notes in the Association should contain the shared segment info as calculated by the vendor.

There are two views for this gramplet. The default view is all of the chromosomes with all of the segments, painted in the order of the Association. The second view is a detailed view of a single chromosome, with each associated person having a separate row. The user clicks on the chromosome label (y-axis) to switch to the detailed view and clicks on the background to return to the default view.

You can install the DNA Segment Map Gramplet on the bottombar of one of the people or relationship 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 or attached to a Citation in the Association with the shared DNA segment data.
    • The format of the Note is a comma separated list or a tab separated list in the order: Chromosome Number, Start Segment, End Segment, shared length in centiMorgans (cMs), SNP (optional), M or P or U (unknown) to override the Maternal Paternal chromosome as determined by the closest genetic connection in the tree (optional). .
    • e.g.: 3,56950055,64247327,10.9,1404 Which means; Chromosome Number: 3, Start Segment: 56950055, End Segment: 64247327, shared length in cMs: 10.9, matching SNPs: 1404
    • 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 ending number for the segment location.
Shared length in cMs
The Genetic Distance (otherwise known as the number of centiMorgans) in the segment.
SNP
optional field of the matching SNPs (Single Nucleotide Polymorphism) in the segment.
M/P flag
optional field to override the Maternal or Paternal or Unknown chromosome. Valid entries are M or P or U. Any other data is ignored


Getting the chromosome data

Sites like GEDmatch make this shared chromosome data available. Direct copy from the GEDmatch results page (with header and tab separators) will work. There can be additional Associations between Person A and Person C (et cetera) as known.

DNApainter provides a description of how to get the chromosome data from many of the common sites.

Legend

Legend with rollover tooltip
  • 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.
  • 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.

Navigation

  • The Legend on the right side lists each associated person who has a mapped segment. Hovering over the legend items will show a tooltip for possible action. Primary button click will change the active person. Secondary button click will open the Person Editor for the associated person.
  • Hovering over the Y-axis chromosome labels will show a tooltip for possible action. Primary button click will switch view to single chromosome of the label clicked. To return to full view, click on the background in the single chromosome view.
  • Hovering over a segment provides detail on the segments at that location. If there are multiple segments overlapping, all will have details.

Configuration

The config file for this gramplet has the following options. Remove the comment (double semi-colon) and edit as needed. Changes are not reflected until the next time the gramps is started. 

[map]
;;chromosome-build=37
;;legend-single-chromosome-y-offset=25
;;legend-swatch-offset-y=0
;;maternal-background=(0.833, 0.845, 0.92)
;;paternal-background=(0.926, 0.825, 0.92)
;;show_associate_id=1
  • Chromosome Build: choose the specific build for the chromosomes. Options are 36, 37, 38.
  • Legend Single Chromosome Y offset: Adjust the height of the legend for the single chromosome view. This may be needed if more than 12 people share the chromosome.
  • Legend Swatch Offset: Offset for the color swatch in the legend. Should be 5 for Windows systems. 0 works for Linux and Mac
  • Maternal Background Color: RGB values for the background of the Maternal Chromosome
  • Paternal Background Color: RGB values for the background of the Paternal Chromosome
  • Show Associate ID: To remove the ID on the legend and tooltip, set to 0. Otherwise leave as 1 to print the Associate ID.


DNA Example data

To reproduce the illustration with the Example.gramps dataset, create two records in the Associations tab in the Person Editor for Luther Robinson(I0656).

The first record is DNA type, adding an association with Robert F. Garner (I1123).
The Note under this association contains the following text: 

Chromosome,Start Location,End Location,Centimorgans,Matching SNPs,Name,Match Name
3,56950055,64247327,10.9,375,Luther Robinson, Robert F. Garner
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 record is also DNA type, adding an association with Maude Garner (I0651).
The Note under this association contains the following text: 

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
Tango-Dialog-information.png
DNA match row data must be in a specific CSV order

The data may include a header but the Gramplet does not require one. Headers are to make the rows more readable by humans. The rows do not need to be sequentially ordered by the chromosome identifier (1 to 22 and X).


Addon-DNA-GEDmatch.png

Sample GEDmatch output (see screenshot) that can be cut and paste into the Note. The fields are the same - Chromosome, Start, End, cM, and SNPs. This can be cut/paste from the GEDmatch output directly into the Note for the Association. The header line will be ignored.

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. Set the Note private if you do not want the data printed in reports.

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. 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.

Addon-DNA-SegmentMap2.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-Tooltip2.png

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.

Addon-DNA-SegmentMap-Single.png

Clicking on the Y-axis label for the 6th chromosome, a detailed view is shown. Click on the background to return to the complete view.

Reference Info

Untested Areas

There are areas in the DNA test that are generally not tested as they are not reliable indicators of a match. If you want to visualize these areas, create a dummy person and add an association with the following DNA segments. 

13,1,19020094,0,0
14,1,19067948,0,0
15,1,20004965,0,0
21,1,9922017,0,0
22,1,16055121,0,0

Centromere Areas

Machines have difficulties to read the area around the centromere. There are less SNPs to read, therefore there is higher probability of false positive matches. For example, if you have a match exactly around the centromere, then it is most probably a false positive match. If you want to visualize these areas, create a dummy person and add an association with the following DNA segments. 

1,121535434,124535434,0,0
2,92326171,95326171,0,0
3,90504854,93504854,0,0
4,49660117,52660117,0,0
5,46405641,49405641,0,0
6,58830166,61830166,0,0
7,58054331,61054331,0,0
8,43838887,46838887,0,0
9,47367679,50367679,0,0
10,39254935,42254935,0,0
11,51644205,54644205,0,0
12,34856694,37856694,0,0
13,16000000,19000000,0,0
14,16000000,19000000,0,0
15,17000000,20000000,0,0
16,35335801,38335801,0,0
17,22263006,25263006,0,0
18,15460898,18460898,0,0
19,24681782,27681782,0,0
20,26369569,29369569,0,0
21,11288129,14288129,0,0
22,13000000,16000000,0,0
X,58632012,61632012,0,0

To Do

Issues

  • 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.
  • If there are overlapping segments within a maternal/paternal view of a chromosome, only the front (last drawn) will be pickable. The tooltip will still provide the details of the hidden segments. Changing the order of Associations (using the up-arrow and down-arrow) to have the closer relatives before further relatives will fix this.

See also

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