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Adding details on where to get DNA Segment Data
{{languages|Addon:DNASegmentMapGramplet}}
{{Third-party plugin}}
[[File:Addon-DNA-SegmentMap-with-TooltipTooltip2.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]]]]
The {{man label|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 {{man label|DNA Segment Map Gramplet}} on the bottombar of one of the people or relationship category list views.
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.
* Add a Citation to the Association to reference the vendor which provided the segment info. This is not used by the gramplet, but is useful since different vendors will produce slightly different segment info. And some Associated Persons might have data from multiple vendors. In these cases, having a second Association is useful.
* 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: <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.For Example: <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>
** Valid entries for each are:
;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
{{-}}
[https://dnapainter.com/help/matchdata DNApainter] provides a description of how to get the chromosome data from many of the common sites.
Add the kit number or other unique info as an Attribute to the Associated Person. For example, create an Attribute 'GEDmatch kit' to contain the GEDmatch kit number. Or 'DNAkit' for the FTDNA kit number. These are not used by the gramplet but good for reference.
The sites that have DNA segment data and formats are covered below.
==== FamilyTreeDNA ====
FamilyTreeDNA provides a download CSV file. Sample format starting at field 2 is set for copy into this gramplet.
<pre>
Match Name,Chromosome,Start Location,End Location,Centimorgans,Matching SNPs
MATCH NAME, 1,191870504,201977600,9.505878,2391
</pre>
==== GEDmatch ====
GEDmatch provides a cut-paste option for data. The format is set for copy into this gramplet. The gramplet will accept either comma or period as the thousands separator.
{| class="wikitable"
|-
| Chr||B37 Start Pos'n||B37 End Pos'n||Centimorgans (cM)||SNPs||Segment threshold||Bunch limit||SNP Density Ratio
|-
| 6||67,249,077||91,039,808||15.6||978||191||114||0.1
|}
==== MyHeritage ====
MyHeritage provides a download CSV. The fields need to be adjusted (remove the 1st, 2nd, 6th and 7th fields).
<pre>
<U+FEFF>Name,Match Name,Chromosome,Start Location,End Location,Start RSID,End RSID,Centimorgans,SNPs
User Name,Match Name,2,172775482,208500311,rs116868713,rs9288384,29.8,16512
</pre>
==== Geneanet ====
Geneanet provides a download CSV that needs to be adjusted. Fields 4 (Number of SNPs) and 5 (Length in centimorgan) need switched and field 6 removed. Semicolon delimeter needs replaced with comma.
<pre>
Chromosome;Start of segment;Length of segment;Number of SNPs;Length in centimorgan (cM);Type of segment
9;14037831;73101159;6804;38.64;half-identical
</pre>
===Legend===
* 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.
* To change the location of the Legend, edit the config file parameters:
<pre>
legend-single-chromosome-y-offset=25
legend-swatch-offset-y=0
</pre>
===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.
<pre>
[map]
;;chromosome-build=37
;;legend-single-chromosome-y-offset=25
;;legend-swatch-offset-y=0
;;maternal-background=(0.833, 0.845, 0.92, 1.0)
;;paternal-background=(0.926, 0.825, 0.92, 1.0)
;;show-centromere=0
;;show_associate_id=1
</pre>
* 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 Centromere: If 1, do not paint the background area for the centromere. This area is dependent on the Build.
* Show Associate ID: To remove the ID on the legend and tooltip, set to 0. Otherwise leave as 1 to print the Associate ID.
===Single Chromosome View===
To view just a single chromosome, click on the chromosome number. This view has each association as a different row, helping to see overlapping areas. To return to the standard view, click on the background area.
===DNA Example data===
The first record is DNA type, adding an association with Robert F. Garner (I1123).<br />
The Note under this association contains the following text:. The last two fields with the names are ignored.
Chromosome,Start Location,End Location,Centimorgans,Matching SNPs,Name,Match Name
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 ===
[[File:Addon-DNA-Note-Example.png|thumb|600px|right]]
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.
{{-}}
[[File:Addon-DNA-SegmentMapSegmentMap2.png|thumb|600px|right]]
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.
{{-}}
[[File:Addon-DNA-SegmentMap-with-TooltipTooltip2.png|thumb|600px|right]]
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.
{{-}}
[[File:Addon-DNA-SegmentMap-Single.png|thumb|600px|right]]
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.
<pre>
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
</pre>
=== 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, edit the config file as described above and set show-centromere to 1. The area of the centromere id dependent on the Build (36, 37, or 38). For example, the list for Build 37 (the most common) is
<pre>
1 121500000 128900000
2 90500000 96800000
3 87900000 93900000
4 48200000 52700000
5 46100000 50700000
6 58700000 63300000
7 58000000 61700000
8 43100000 48100000
9 47300000 50700000
10 38000000 42300000
11 51600000 55700000
12 33300000 38200000
13 16300000 19500000
14 16100000 19100000
15 15800000 20700000
16 34600000 38600000
17 22200000 25800000
18 15400000 19000000
19 24400000 28600000
20 25600000 29400000
21 10900000 14300000
22 12200000 17900000
X 58100000 63000000
</pre>
To view the centromere for all chromosomes, edit the config file to change this option:
<pre>
show-centromere=1
</pre>
= 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. If it is completely obscured, you The tooltip will not be able to see still provide the details of the hidden segmentsegments. Changing the order of Associations (using the up-arrow and down-arrow) to have the closer relatives before further relatives will fix this. To see overlapping segments, select a single chromosome.
= See also =
* DNA Segment Map gramplet #469 550 (GitHub pre-release [https://github.com/gramps-project/addons-source/pull/469 Pull 469550])
* [[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 DNAgrampleDNAgramplet]
* [[Gramps_{{man version}}_Wiki_Manual_-_Entering_and_editing_data:_detailed_-_part_1#Associations|Introduction to Associations in Gramps]]
* [[Roles, Relationships & Associations]]
