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I have a DNA file from tellmeGen and was wondering whether I can convert the file to an ancestryDNA, FTDNA, MyHeritage or similar file format in order to upload it to myHeritage, FTDNA or DNA.Land for further investigation?

The DNA file from tellmegen is a csv file and has the following first six lines (separated by a space):

# rsid  chromosome  position    genotype
rs991757223 1   100177980   DD
rs967277439 1   108681808   DD
1KG_1_109440678 1   109440678   DD
rs750385149 1   109479801   DD
rs780371591 1   110655430   DD

However, if I change the above csv to txt with a simple text editor (on a mac if this matters) and change the header (here in the FTDNA version) the upload to any of the above websites does not function.

I use this table to guide me with the output format (via http://www.beholdgenealogy.com/blog/?p=2700).

enter image description here

This would be an example for the first two lines in a FTDNA file format:

RSID,CHROMOSOME,POSITION,RESULT
"rs991757223","1","100177980","DD"

However, it seems that simply adding the header and change the data output format does not function. Why? How can I adjust my DNA file so that I can upload it to other DNA websites?

P.S.: I was only able to upload the original file from tellmeGen to GEDMatch without any adjustments.

Edit:

After ordering the file by group (column 2), the order of the data looks (abbreviated) like this:

200610-10   0   0   AA
200610-108  0   0   AA
200610-109  0   0   AA
...
2010-08-MT-655  0   0   GG
2010-08-MT-664  0   0   AA
2010-08-MT-773  0   0   AA
...
exm-rs10862691  0   0   GG
exm-rs11136341  0   0   AG
...
indel.101007    0   0   II
indel.101499    0   0   II
...
kgp2443711  0   0   GG
kgp24661105 0   0   GG
...
rs10177008  0   0   AG
rs10178695  0   0   AG
...
rs41369547  MT  12669   GG
rs193302956 MT  12705   GG
...
rs200665918 XY  1484071 GG
rs200082252 XY  1484097 GG
...
rs2694717   X   3140992 AA
rs17051551  X   3142375 AA
...
rs34961774  Y   6033626 AC
rs34448815  Y   6033653 --
...
rs145303326 1   12378223    GG
rs150598243 1   12378274    GG
rs141044837 1   12379557    GG

Shall I remove the "noise" of the first lines?

3

It is not all that simple to convert to an FTDNA file. There are a few things that might be tripping you up.

From your example, you seem to indicate that the first data line in your tellmeGen file is for position 100177980 on chromosome 1. Check that the lines are ordered by chromosome and position number, and that lower positions are before higher positions. I'm worried that tellmeGen did not order your positions numerically, but alphabetically, i.e. 100 is followed by 20 which is followed by 3, when it should be 3, 20, 100. If that's the case, you'll have to sort the data lines correctly.

It looks to me like the tellmeGen file has tabs between the fields, but FTDNA uses a comma. Also FTDNA needs double quotes around each field. So if you're using just a text editor, then convert all the tabs to "," and then insert a " at the beginning of each line and a " at the end of each line.

Then add as the first line the FTDNA header: RSID,CHROMOSOME,POSITION,RESULT

FTDNA also requires the same header between chromosome 22 and 23. And make sure your chromosome 23 is named "X", e.g. in my FTDNA file lines 702457 to 702462:

"rs5771007","22","49542594","TT"
"rs3888396","22","49558258","TT"
RSID,CHROMOSOME,POSITION,RESULT
"rs17883004","X","1370495","AA"
"rs5939319","X","2710157","AA"
"rs1419931","X","2713633","GG"

My FTDNA files also have Unix line terminators of LF (linefeed), whereas Windows text files have line terminators of CRLF (carriage-return + linefeed). I don't know if the line terminator needs to be changed for an upload, but if necessary, most text editors should be able to change your line terminator for you.

If you do all the above and you still can't get the upload as an FTDNA file to work, I'd suggest you try instead using the 23andMe raw data file format. It is much closer to your original file, being text format, using tabs between fields and not requiring double quotes around fields.

Try taking your original file, replacing the first header line with the following description and header line:

# This data file generated by 23andMe at: Mon Jan 15 10:49:09 2018
#
# This file contains raw genotype data, including data that is not used in 23andMe reports.
# This data has undergone a general quality review however only a subset of markers have been 
# individually validated for accuracy. As such, this data is suitable only for research, 
# educational, and informational use and not for medical or other use.
# 
# Below is a text version of your data.  Fields are TAB-separated
# Each line corresponds to a single SNP.  For each SNP, we provide its identifier 
# (an rsid or an internal id), its location on the reference human genome, and the 
# genotype call oriented with respect to the plus strand on the human reference sequence.
# We are using reference human assembly build 37 (also known as Annotation Release 104).
# Note that it is possible that data downloaded at different times may be different due to ongoing 
# improvements in our ability to call genotypes. More information about these changes can be found at:
# https://you.23andme.com/p/9ea93ca016155efc/tools/data/download/
# 
# More information on reference human assembly build 37 (aka Annotation Release 104):
# http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9606
#
# rsid  chromosome  position    genotype

If you use 23andMe format, then use X for chromosome 23, and use Y and MT for any Y-DNA and mitochondrial data that tellmegen might be including.

Give the file you create in 23andMe format a name something like:

genome_your_name_v5_Full_20180115104908.txt
  • Thank you, Ikessler, for you extensive answer. :) One short remark: can you please tell me how the 23andMe data is ordered? Is it ordered alphabetically or as the FTDNA format? As well, I updated the snippet of my DNA file so you can see in which way the tellmeGen file is ordered. As you can see, I have some different characters like 1KG_1_109440678 in it. Do I need to delete them? – Til Hund Oct 16 at 7:18
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    23andMe raw data is ordered like the FTDNA format, by chromosome and position number. The 1KG... is RSID, which is the name tellmegen assigns to the SNP. I believe most companies ignore the RSID field when uploading and just use the chromosome, position and genotype, so you shouldn't have to change that field. – lkessler Oct 16 at 18:21
  • Hi Ikessler, I did as you told me and ordered the file, added the header and rename the file to no avail. It is still not recognised. When I ordered the file, then 'Y' and 'MT' and 'X' do stand at the top or shall they go after the numerical chromosomes (see edit in original post)? – Til Hund Oct 19 at 18:55
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    Til: Yes, definitely remove the chromosome 0's and XY's. Put the X's at the end, after chromosome 22. Also you shouldn't have to include the Y's and MT's at all, since autosomal uploads don't use them. If you include them, Y is after X and MT is after Y. Also 23andMe only has one value for X (if you're a male), Y and MT. i.e. Don't put GG, just put G. If the two differ, put two dashes, i.e. "--" – lkessler Oct 20 at 14:10
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    I meant if the two letters differ, e.g. CG, then it was not read properly since there is only one chromosome so put in "--" to represent a no-call or don't include the line. If they are the same, show only one letter. This is only for single chromosomes in 23andMe raw data. – lkessler Oct 20 at 21:21

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