Improve MT DNA and Y DNA Haplogroups (only 23andme RAW files)


If you and your close family are tested in 23andme you might tried to get a better / precise haplogroup definition using James Lick and Morley haplogroup predictors, and you might find sometimes the haplogroup prediction “matching values” may differ from one raw to another. This happens due to the genotyping technology, that sometimes may incur in “no calls” issues, that is, the technology was not able to read properly a specific position of your DNA.

Given the fact that YDNA and MTDNA pass from a parent to children as perfect copy from one to another, there is a chance to merge this no calls DNA markers to get a better definition of your haplogroups.

So, there is a method to improve the quality of your MTDNA and YDNA haplogroups. This method is based on merging two or more raws that contains the same haplogroup (as mother to children or father/gparents to sons) using DNA Kit Studio.

There are two main rules that must be precisely followed in order to avoid incorrect haplogroup results.

MTDNA

Only the direct mother line can be merged. That is, one can merge gmother’s raws, mother with the children ones from the same female’s line. You must not merge father or gfather’s raw files due to MT DNA is passed from females to children.

YDNA

Only the direct father’s line can be merged. That is, one can merge gfather’s / father’s raw files with the sons from the same father’s line. You must not merge father / gfather’s that are not direct descendants. But, there is an exception, full siblings of any man from the father descendants can be merged to the target one, for example, father’s brother raw file merged with father’s son raw file.

Instructions

  1. Download and unzip DNA Kit Studio
  2. Unzip your RAW files:
    1. 23andme: Use the RAW TXT file (something like genome_XXXX.txt)
  3. Open DNA Kit Studio and in the Merge RAW Files group choose:
    1. Raw Data First: One of the RAW file to merge
    2. Raw Data Second: The other RAW file to merge
    3. Raw Data Output: Choose a filename and the for the outputfile
    4. Output Format: Choose as output format 23andme
    5. Merge SNPs: Left checked
  4. Click on Merge button and wait until the process is finished
  5. Repeat the process as many times as remaining RAWs files there are, just keeping in mind to set as RAW Data First the one that was generated in the step 4.
  6. Finally, upload your “improved” raw file to:
    1. MT DNA, upload to James Lick (predictor de mtDNA)
    2. Y DNA, upload to Morley (predictor de yDNA).

Enjoy it!

Donation

Feel free to use it. If you like this tool and you would like to help me to continue developing DNA tools, I would appreciate any amount of donation:

Thanks for the donation