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Update Usage
=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.
You can install the {{man label|DNA Segment Map Gramplet}} on the bottombar of one of the people or relationship category list views.
* 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: <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)</code>. ** ege.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>
** Valid entries for each are:
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===Getting the chromosome data ===
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 on of how to get the chromosome data from many of the common sites.
===Legend===
[[File:Addon-DNA-SegmentMap-legend.png|thumb|338px|right|[ {{man label|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.
* 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.
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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=== Example ===
[[File:Addon-DNA-Note-Example.png|thumb|600px|right]]
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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[[File:Addon-DNA-Association-Example.png|thumb|600px|right]]
Save the Association.
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[[File:Addon-DNA-Associations-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.
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[[File:Addon-DNA-SegmentMap.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.
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[[File:Addon-DNA-SegmentMap-with-Tooltip.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.
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== 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, create a dummy person and add an association with the following DNA segments.
<pre>
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
</pre>
= To Do =
* Add an optional M / P flag for each input line to override the Maternal / Paternal determination.
* Add the start and stop values per line for the tooltip.
* Add the relationship and the common ancestor to the tooltip.
* Grey out the paternal X chromosome for males.
= Issues =
= See also =
* DNA Segment Map gramplet #469 (GitHub pre-release [https://github.com/gramps-project/addons-source/pull/469 Pull 469])
* [[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]]
[[Category:Plugins]]
[[Category:Addons]]
