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CuriousAboutStuff
07-03-2017, 07:06 PM
Each time I download the file, it does so in a strange format and I'm having some problems uploading it then. I think it's a .vcf file.

07-03-2017, 07:12 PM
Yes to gedmatch genesis, the beta platform, we discussed this in your problem thread, probably better though to wait until they release their new format, .txt could be a little while though.

ajc347
07-03-2017, 07:14 PM
You can upload the Living DNA vcf file to Gedmatch Genesis beta but not the main Gedmatch site. The link for the Genesis page is on the main Gedmatch site.

EDIT: It looks like sgdavies and I were posting a reply at the same time. :)

CuriousAboutStuff
07-03-2017, 07:47 PM
Thank you both. Seems I wasn't uploading it through genesis

Kathlingram
07-04-2017, 11:24 AM
Thank you both. Seems I wasn't uploading it through genesis

There is already at least two threads on here about that..this one discusses some limitations on doing it right now.. their download is erroneous for some newer testers
http://www.anthrogenica.com/showthread.php?11132-Problems-downloading-raw-data-file-from-LivingDNA

CuriousAboutStuff
07-04-2017, 10:45 PM
There is already at least two threads on here about that..this one discusses some limitations on doing it right now.. their download is erroneous for some newer testers
http://www.anthrogenica.com/showthread.php?11132-Problems-downloading-raw-data-file-from-LivingDNA

Apologies.

I'm just going to wait until they release their text format.

Kathlingram
07-05-2017, 04:21 PM
I got this today :"In accordance from feedback from the community, our raw data files are currently undergoing an overhaul, so autosomal downloads may be unavailable during this time. We expect that they'll be back within the month.
Thank you for bearing with us."

ollie444
07-05-2017, 04:24 PM
I got this today :"In accordance from feedback from the community, our raw data files are currently undergoing an overhaul, so autosomal downloads may be unavailable during this time. We expect that they'll be back within the month.
Thank you for bearing with us."

I assume this means that they are missing their 10th July target for releasing the txt version.

jortita
07-11-2017, 04:20 AM
They seem to be delayed on the text file downloadable version, it was due 10 July

lilac9
07-11-2017, 05:56 PM
I just got the e-mail today and I downloaded it to Gedmatch genesis. It's working!

jortita
07-12-2017, 03:12 AM
I found the text file and also received a response from Living DNA. It seems they are working on improving the raw data download file as the current text file similar to the vcf file has extremely low genotyping rates for Gedmatch calculators. I am not sure how accurate results are if genotype rates are only 3000-15000 SNPs across all calculators

timberwolf
07-12-2017, 03:29 AM
Just uploaded the text file on to Gedmatch.

So July 10th was about right, give or take a day or two.

sktibo
07-12-2017, 04:12 AM
I found the text file and also received a response from Living DNA. It seems they are working on improving the raw data download file as the current text file similar to the vcf file has extremely low genotyping rates for Gedmatch calculators. I am not sure how accurate results are if genotype rates are only 3000-15000 SNPs across all calculators

Good to hear, and thanks for asking them about that. My Living DNA upload shows much fewer SNPs than Ancestry, FTDNA, and 23andme kits on Gedmatch calcs. my "Big Three" Gedmatch results are consistent despite their slight differences, but the Living DNA upload is bordering on looking like a different individual altogether, so I don't think it is ready yet.

jortita
07-12-2017, 05:45 AM
I have also managed to upload the file onto regular Gedmatch. Sktibo, I agree as my oracle results as well as calculator results are very different from Ancestry DNA, FTDNA and MyHeritage DNA

ollie444
07-12-2017, 10:12 AM
Good to hear, and thanks for asking them about that. My Living DNA upload shows much fewer SNPs than Ancestry, FTDNA, and 23andme kits on Gedmatch calcs. my "Big Three" Gedmatch results are consistent despite their slight differences, but the Living DNA upload is bordering on looking like a different individual altogether, so I don't think it is ready yet.

My ancestry kit: 17501and my livingdna kit on k13: 17502

Pylsteen
07-12-2017, 10:28 AM
The text file seems to include the x-chrom, which did not occur int the vcf, interesting.
also: number of shown SNP's seems different, or less; in chromosome painting it seems more "blocky".

ok: some first tests, left genesisgedmach, right gedmatch

Eurogenes K13, Genesis, Gedmatch
North_Atlantic 42,69 42,51
Baltic 23,63 23,78
West_Med 14,96 15,02
West_Asian 6,69 6,78
East_Med 4,84 4,77
Red_Sea 0,48 0,45
South_Asian 1,29 1,1
East_Asian 4,28 4,29
Siberian 0,14 0,19
Oceanian 0,75 0,76
Sub-Saharan 0,27 0,35

JTest: Ashkenazi 4,16 (gedmatch) vs. 4,44 (genesis). Most likely reason in my mind: inclusion of the X-chrom in gedmatch, which I inherited from my non-Jewish mother.

predicting eye color test: lots of melanin-adding alleles > brown = correct

Pylsteen
07-12-2017, 09:02 PM
Though my knowledge about DNA is fine, I am still struggling with interpreting the raw data file comparing to SNP libraries, in particular, the letters, for example:

LivingDNA gives me:

rs916977(TT), which is apparently connected with brown eyes; SNPedia, however, lists variants AA, AG and GG, which then must be the mirrored letters, I assume.

I also looked at one of the "baldness" genes on the X-chrom. Here, LivingDNA gives me:

rs1385699(C). I am totally not sure if I have to interpret this as C or as its mirrored G. *(Yes, I want to know if I inherited from my bald maternal grandfather, or from my less bald grandmother's family)*.

Edit:

O, I see I get the hang of it. It seems that sometimes they tested the original string, sometimes the derived one. If I see CC but the SNPedia etc. only mentions GG, than I have to go with that one. (C<>G, and A<>T, I remember "round letters with each other", "pointy letters with each other").

Nice to play with it. Now I found out I belong to "genoset 246", which gives a "neutral" Alzheimer risk. Interesting.

Pylsteen
07-13-2017, 09:09 AM
There seem to be problems with tokenization and batch processing in gedmatch;
in the DNA file diagnostic feature, it shows "Warning: Kit will not be included in batch processing. It does not have enough SNPs."

juniper
07-13-2017, 11:27 AM
I have uploaded my LivingDNA and ftDNA to gedmatch (not genesis) I’ve done the one-to-one with a match of mine using both LivingDNA and ftDNA.
Results:
ftDNA Chr 1 > 238,713,564 - 243,487,380, cM 13.4, SNPs 973
ftDNA Chr 4 > 71,411,418 - 99,746,595, cM 25.4, SNPs 3131

LivingDNA Chr 4 > 68,401,147 - 99,714,483, cM 27.8, SNPs 997.


LivingDNA resulted in nothing on Chr1 (using default min 7 segment size) and low SNPs on Chr4 compared to the ftDNA result.

ollie444
07-13-2017, 03:55 PM
I have uploaded my LivingDNA and ftDNA to gedmatch (not genesis) I’ve done the one-to-one with a match of mine using both LivingDNA and ftDNA.
Results:
ftDNA Chr 1 > 238,713,564 - 243,487,380, cM 13.4, SNPs 973
ftDNA Chr 4 > 71,411,418 - 99,746,595, cM 25.4, SNPs 3131

LivingDNA Chr 4 > 68,401,147 - 99,714,483, cM 27.8, SNPs 997.


LivingDNA resulted in nothing on Chr1 (using default min 7 segment size) and low SNPs on Chr4 compared to the ftDNA result.

my comparison between my ancestry kit and my living dna kit uses 157039 SNPs.

Pylsteen
07-14-2017, 10:26 PM
I found the text file and also received a response from Living DNA. It seems they are working on improving the raw data download file as the current text file similar to the vcf file has extremely low genotyping rates for Gedmatch calculators. I am not sure how accurate results are if genotype rates are only 3000-15000 SNPs across all calculators


I only see this now; good that they are aware of this problem, hope they are working on this; it's important, since the file can't be batch processed on gedmatch now due to its size.

btw, I'm struggling uploading a Gedcom to Gedmatch; it does work properly, but it seems to squeeze the names into 25 characters max, which makes many names very uncomplete, not convenient at all. I know gedcom has some character limits, though I saw many other gedcom files containing names longer than 25 characters, and in notepad the names are fully written, so I don't know what is going wrong there.. well, that's my own file problem, I suppose.:\

Kathlingram
07-14-2017, 10:31 PM
1755317554


So this is the comparison between 23andme and Living DNA of Eurogenes..

and my matches don't make a lot of sense.. some people I know I match do not share chromosomes when I do the one to one there.. What exactly is being matched? Shared Ancestors like everywhere else?
Thanks for help

jortita
07-15-2017, 02:32 AM
I only see this now; good that they are aware of this problem, hope they are working on this; it's important, since the file can't be batch processed on gedmatch now due to its size.

btw, I'm struggling uploading a Gedcom to Gedmatch; it does work properly, but it seems to squeeze the names into 25 characters max, which makes many names very uncomplete, not convenient at all. I know gedcom has some character limits, though I saw many other gedcom files containing names longer than 25 characters, and in notepad the names are fully written, so I don't know what is going wrong there.. well, that's my own file problem, I suppose.:\

I am not familiar with Gedcoms, I have never uploaded one

Kathlingram
07-15-2017, 01:11 PM
1755317554


So this is the comparison between 23andme and Living DNA of Eurogenes..

and my matches don't make a lot of sense.. some people I know I match do not share chromosomes when I do the one to one there.. What exactly is being matched? Shared Ancestors like everywhere else?
Thanks for help

SO No One answered me but it says THIS at Gedmatch Genesis :
" Are you puzzled by the new, very close, match you are seeing with somebody. Does it have "Exome" in the name? Even if it does not say "Exome", there are a few "Exome" kits on Genesis. Exome kits are different than the "genealogy" kits we are used to dealing with. The exome regions of the chromosome have much less difference from one individual to the next. Because of that, they appear as close matches to more people.

We apologize for the "false match". We plan to provide some means of differentiating these "exome matches" from the real thing, but it will take a while to get it in place.

Pylsteen
07-15-2017, 02:17 PM
We apologize for the "false match". We plan to provide some means of differentiating these "exome matches" from the real thing, but it will take a while to get it in place.


I'm not sure, but it is often that matches from the one-to-many list are not matches when "verified" through one-to-one match. Maybe the algorithm selects "possible matches" for the one-to-many list.

Kathlingram
07-15-2017, 03:33 PM
I'm not sure, but it is often that matches from the one-to-many list are not matches when "verified" through one-to-one match. Maybe the algorithm selects "possible matches" for the one-to-many list.

No that is NOT what they are saying I do not think.. I AM told THIS :"cross platform matching is a serious problem, not just at Gedmatch, but also at commercial testing companies like FTDNA and 23andme" ( quoting a member here.. he knows lol)

I almost NEVER do not see a One to One who does not match me.. I Beta Tested with the Owners of Gedmatch years ago from my 23andme account..

I THINK they are saying THIS:"exome regions of the chromosome have much less difference from one individual to the next. Because of that, they appear as close matches to more people."

EXOME being the Operative word that I do not exactly understand but I follow what they are saying..

I am NOT a Scientist at all but my graduate degree is Anthropology so I understand populations and migrations pretty good

Kathlingram
07-15-2017, 09:10 PM
No that is NOT what they are saying I do not think.. I AM told THIS :"cross platform matching is a serious problem, not just at Gedmatch, but also at commercial testing companies like FTDNA and 23andme" ( quoting a member here.. he knows lol)

I almost NEVER do not see a One to One who does not match me.. I Beta Tested with the Owners of Gedmatch years ago from my 23andme account..

I THINK they are saying THIS:"exome regions of the chromosome have much less difference from one individual to the next. Because of that, they appear as close matches to more people."

EXOME being the Operative word that I do not exactly understand but I follow what they are saying..

I am NOT a Scientist at all but my graduate degree is Anthropology so I understand populations and migrations pretty good

Actually further thought is that I do not understand EXOME at all unless it refers to distant or ancient segments used for ethnicity estimation which if not thrown out ( like AncestryDNA does) can make two people appear more closely related..Thoughts??

Pylsteen
08-01-2017, 11:32 AM
Well, I finally managed to upload a gedcom, 9 generations, in which the names were not brutally shortened by switching to another genealogy program (a few names are still too long.. but I'm fairly happy). I have much more info, but 9 generations seem good enough to me. Only problem remains DNA file itself..

Amerijoe
08-01-2017, 11:37 AM
Here is Debbie Kenneth's take on Gedmatch and Livingdna. This explains low snp count and compatibility.

https://cruwys.blogspot.co.uk/2017/07/living-dna-updates-and-gedmatch-genesis.html

Kathlingram
08-01-2017, 11:42 AM
Here is Debbie Kenneth's take on Gedmatch and Livingdna. This explains low snp count and compatibility.

https://cruwys.blogspot.co.uk/2017/07/living-dna-updates-and-gedmatch-genesis.html

Debbie, as a member of ISOGG has been instrumental as a liason with Living_DNA. She is very knowledgeable about this GSA chip and it's uses

Pylsteen
08-01-2017, 11:45 AM
Here is Debbie Kenneth's take on Gedmatch and Livingdna. This explains low snp count and compatibility.

https://cruwys.blogspot.co.uk/2017/07/living-dna-updates-and-gedmatch-genesis.html


Cooll. Also interesting what she writes:


A big update to our admixture results can be expected by the end of the year as more reference datasets are added to the collection. They will be including data from the Symons Genome Diversity Project, data from Asia and data from Aboriginals in Australia. Their Irish DNA Research Project is going well and they already have 1200 samples. They now have 450 people in their German DNA Research Project. Further projects are planned for France, Portugal, Austria, Belgium and the Netherlands.


Now these project take a long time... however, they released the complete mode and the raw data without (much) delay, which is good, I suppose.

Kathlingram
08-07-2017, 09:09 PM
I had seen that you could upload other tests to Gedmatch Genesis and see what the Overlap is.. how does one do that? I did put my AncestryDNA kit on it.. I CAN do one to one I think but not sure who you read the overlap

Pylsteen
08-07-2017, 09:20 PM
I think you can just do that in the one to many list?

Kathlingram
08-07-2017, 09:27 PM
I think you can just do that in the one to many list?

It did not yet populate there yet I guess..

Kathlingram
08-08-2017, 07:03 PM
I think you can just do that in the one to many list?

This is what mine looks like compared against myself
It says 1.2 generation so does that mean .2 generation of difference?

Says this:"Total Half-Match segments = 1749.9 cM (48.8 Pct)
Total Full-Match segments = 793.0 cM (22.1 Pct)
Total of all matching segments > 7 cM = 2542.9 cM (70.9 Pct)
Estimated number of generations to MRCA = 1.2
150101 SNPs used for this comparison."

Doing it the other way I think it says 75. Pct total.. is that what I should be looking at?
Edited I do see difference in matches between the two tests and I just saw some information that 23andme has started using a new chip called V5..assuming it is the GSA chip

Dibran
08-09-2017, 12:34 AM
Cooll. Also interesting what she writes:




Now these project take a long time... however, they released the complete mode and the raw data without (much) delay, which is good, I suppose.

Do they plan to eventually do a south/southeast europe project to gather southern european DNA? it would add more accuracy to south east europeans like myself.

sktibo
08-09-2017, 01:42 AM
Eventually they want to do the entire world in more detail, but the countries they have listed are the ones that will be done in the foreseeable future

Dibran
08-09-2017, 06:04 PM
Eventually they want to do the entire world in more detail, but the countries they have listed are the ones that will be done in the foreseeable future

I see thank you. Will they take free volunteers for projects from volunteers outside their country of origin?

I definitely want to get my uncle and some of my cousins tested should s southeast European project be undertaken.

FionnSneachta
08-09-2017, 07:38 PM
I see thank you. Will they take free volunteers for projects from volunteers outside their country of origin?

I definitely want to get my uncle and some of my cousins tested should s southeast European project be undertaken.

I doubt that they will take free volunteers since they haven't done it for the other projects. It would encourage more people to do it since a lot may qualify but may have no interest and then having to pay for it on top of that automatically deters a lot of people. However, free autosomal DNA transfer should be introduced before those projects start so if someone has tested with a previous company they should get the results for free.

Kathlingram
08-09-2017, 10:17 PM
Debbie Cruwys Kennett is again posting at All Genetic Genealogy about the GSA chip which 23andme apparently began using in May or just before..

Some of my Gedmatch Genesis matches and I have been comparing notes and we can see that whichever kit we are using at Genesis..we DO match but the size varies between the kits used.
One has a 5.5 GD match with me when both Living_DNA kits are used.. and it drops down to 7.6 GD when it is her L_D vs my AncestryDNA kit.. however the match exists still..

Different people have a different interpretation of what the difference is but am not sure anyone at this time knows exactly.. Debbie has not put anything at Gedmatch Genesis except her L_D kit so she did not know how to measure overlap.Ann Turner has posted also..but this is quite new..

It seems that many other kits do not overlap well.. it may be that my AncestryDNA does not..

My 23andme kit is the V3 and it would not load.. 23andme ( who did NOT announce this Chip being used)plans an upgrade at some point..

I was a Beta Tester when 23andme went live in 2009 and that was V2 which was upgraded to the V3.. I feel sure I will upgrade if it is reasonable..I do Admin several groups at FTDNA and not at all sure what they will do.. They had a difficult time imputing the 23andme V4 and Ancestry DNA latest chip.. Those transfers ( thousands of them) only usually start at 4th cousin and up.. I have moved all my folks that will transfer in but none of us tested Family Finder..

Kathlingram
10-10-2017, 06:35 PM
I was away for a few days..checking my DNA I see that Gedmatch now supports "People who match one or both of 2 kits" I further see a prominent person matching me who I am pretty sure we never did that ( Beta tester 23andme 2009)
I further see that it seems to be on the 23andme V5 Chip..
From that I am deducing that V5 chips with their shorter runs may have errors..
Could mean that "we" are not as close to matching as Q1 2018.. or that serious modifications need to happen

Kathlingram
10-13-2017, 02:11 PM
I was away for a few days..checking my DNA I see that Gedmatch now supports "People who match one or both of 2 kits" I further see a prominent person matching me who I am pretty sure we never did that ( Beta tester 23andme 2009)
I further see that it seems to be on the 23andme V5 Chip..
From that I am deducing that V5 chips with their shorter runs may have errors..
Could mean that "we" are not as close to matching as Q1 2018.. or that serious modifications need to happen
algorithm for cross-platform comparisons when the SNP overlap is low


I was told this:""algorithm for cross-platform comparisons when the SNP overlap is low".. and apparently it is a problem..
I myself am not expecting matching from Living_DNA anytime soon

NEED to delete this one and it won't work

Kathlingram
10-13-2017, 02:12 PM
[QUOTE=Kathlingram;295690]I was away for a few days..checking my DNA I see that Gedmatch now supports "People who match one or both of 2 kits" I further see a prominent person matching me who I am pretty sure we never did that ( Beta tester 23andme 2009)
I further see that it seems to be on the 23andme V5 Chip..
From that I am deducing that V5 chips with their shorter runs may have errors..
Could mean that "we" are not as close to matching as Q1 2018.. or that serious modifications need to happen[QUOTE]


I was told this:""algorithm for cross-platform comparisons when the SNP overlap is low".. and apparently it is a problem..
I myself am not expecting matching from Living_DNA anytime soon

jortita
10-14-2017, 02:33 AM
I was able to upload my Living DNA file to Gedmatch in addition to Gedmatch Genesis. The admix calculators can be run however it seems my kit will not get tokenised