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View Full Version : 23andme V5 or Converted V3 for G25?



ThaYamamoto
03-06-2020, 10:23 PM
I'm wondering which one to send to Davidski, primarily cuz the difference I get in calculator scores between the V5 and converted V3 concern me. I'm of mixed background and my SSA heritage is primarily Nilotic+Pygmy with most calculators when using V5, which normally converts to mostly Bantu+minor Senegambian with the V3. As calculators have been updated over the past few years tho, V5 scores are slowly starting to match V3, but its still a concern cuz I would like to model the African portion of my ancestry the most. My V5 file is hella light, at like 16mb with pathetic overall SNPs tested on most gedmatch calculators but since I deleted my gedmatch acc I can't provide the exact numbers. The V3 convert on the other hand is much larger but if none of this effects something like g25, then obviously Imma just send the v5. I should mention Kurd's SAPDA is the only calculator that has offered me satisfactory results in keeping with known ancestry and the over inflation of South Asian I get across most calculators.

Anyway I've gone off on a big boy tangent, does it matter which one I send?

StillWater
03-06-2020, 11:45 PM
How did you convert v5 to v3?

ThaYamamoto
03-07-2020, 01:13 AM
How did you convert v5 to v3?

OK so you have to download the imputed VCF file that you [already?] have up on DNA.land. Download DNA Kit Studio (from Dnagenics dot com) and go to the VCF tools tab, and go to VCF to RAW converter. Select your imputed VCF file from DNA.land and in the drop down "Raw Data Output" enter the name of the kit your gonna create i.e. genome_XX_YY_V3_FULL_2018.txt. Then select Raw Data Template in the drop down as Template 23andme_v3.txt. Click convert and your done my dude.

edit: If you don't have a kit up on DNA.land obviously just go ahead and upload and wait 4-5 hours for them to impute the file.

StillWater
03-07-2020, 02:04 AM
OK so you have to download the imputed VCF file that you [already?] have up on DNA.land. Download DNA Kit Studio (from Dnagenics dot com) and go to the VCF tools tab, and go to VCF to RAW converter. Select your imputed VCF file from DNA.land and in the drop down "Raw Data Output" enter the name of the kit your gonna create i.e. genome_XX_YY_V3_FULL_2018.txt. Then select Raw Data Template in the drop down as Template 23andme_v3.txt. Click convert and your done my dude.

edit: If you don't have a kit up on DNA.land obviously just go ahead and upload and wait 4-5 hours for them to impute the file.

Downloaded latest version of DNAKitStudio and don't see a drop down menu. What version of DNAKitStudio are you using?

ThaYamamoto
03-07-2020, 05:48 PM
Downloaded latest version of DNAKitStudio and don't see a drop down menu. What version of DNAKitStudio are you using?

I'm not on a Windows machine right now but I'll check it out if you still need help. You could just send your raw data to me or someone else on here and it can be done for you if you'd be cool with that.

Can anyone actually help me out with my question tho??

ThaYamamoto
03-07-2020, 06:06 PM
Nevermind ya'll, I'll just email Davidski, dont know why I didn't think of that before

StillWater
03-07-2020, 11:12 PM
Nevermind ya'll, I'll just email Davidski, dont know why I didn't think of that before

He does post on here.

z000
07-21-2020, 07:53 AM
Now I'm wondering if it could affect the results. I've mailed him with my DnaLAND converted files.

ThaYamamoto
07-21-2020, 04:01 PM
Now I'm wondering if it could affect the results. I've mailed him with my DnaLAND converted files.

Yeah my converted V3 were identical except for the slightest difference in unscaled coordinates. So I don't know if imputation to V3 is all that good tbh. Let us know if yours is significantly different?

Ruderico
07-22-2020, 09:27 AM
Way back when I asked whether David wanted my converted v3 and he said no, so it's probably not worth converting for G25

Ruderico
08-04-2020, 11:19 AM
Did you say some reason why not? Those converted v3 from v5 usually have better results on Gedmatch.

I didn't, I was pretty sure he's aware of that, but G25 isn't gedmatch. My results with converted V3 vs V5 were virtually the same in Gedmatch anyway.

misanthropy
11-10-2020, 04:58 PM
On a related note, I wonder if the 23andme V5.9 update would have an effect on the raw data or it is just a different way 23and interprets the data?

digital_noise
11-10-2020, 06:25 PM
No, it’s just their algorithm was adjusted or updated. Reference pops updated. Raw is the same.