genotype format with 1 to 4

Question

[Mari]

Hi, I am trying to run this software (a bit old ... published in 2009 and the developer seems to be graduated years ago).

https://blog.nus.edu.sg/sshsphphg/varld/

The input genotype file seems to be unfamiliar to me (attached below).

I wonder how do you call this format, and if there is a way to convert vcf file to this format.

I wonder what exactly the 1, 2, 3, and 4 mean (0/0, 0/1, 1/1 and NA?)

Thank you very much.

rs252343    29093865    2   1   2   2   2   1   2   3   1   2   1   1   1   3   1   1   1   1   2   1   1   3   2   2   2   2   3   2   2   1   2   1   2   1   2   1   1   1   1   1   1   1   3   3   1   1   1   1   1   1   2   3   1   1   1   1   2   2   1   1   1   1   1   1   1   1   2   1   2   1   1   1   2   1   2   2   2   2   2   1   2   2   3   1   1   1   1   2   2   2   1   1   1   2   2   4
rs252342    29094079    2   1   2   4   2   1   2   3   1   2   1   1   1   3   1   1   1   1   2   1   1   3   2   2   2   2   3   2   4   1   2   1   2   1   2   1   1   1   1   1   1   1   3   3   1   1   1   1   1   1   2   3   1   1   1   1   2   2   1   1   1   1   1   1   1   1   2   1   2   1   1   1   2   1   2   2   2   2   2   1   2   2   3   1   1   1   1   2   2   2   1   1   1   2   4   1
rs17779364  29095722    3   3   3   2   3   3   3   3   3   3   3   3   3   3   3   3   3   1   2   3   3   3   3   3   3   3   3   3   3   2   3   3   3   2   3   3   2   1   3   2   3   2   3   3   3   3   3   2   2   3   3   3   3   3   3   3   2   2   3   2   3   3   3   2   3   3   3   3   3   3   3   3   3   3   2   3   3   3   2   3   3   3   3   3   2   3   3   3   3   3   3   3   3   3   3   2

Answer 1

[zx8754]

It is stated in the README file:

Genotypes are coded as numerals 1,2,3,4 with 
1 as homozygote AA, 
2 as heterozygote Aa, 
3 as homozygote aa, and 
4 as missing.

I don't know name of this format, and yes, it is possible to convert VCF to this format.

Answer 2

[Mari]

Oh, I may have missed that. Thank you very much!

[Ram]

Hi Mari,

Please do not add answers unless you're answering the top level question. Use Add Comment or Add Reply as appropriate. This reply is better suited as a comment on zx8754's answer. Could you make the appropriate change please? That would involve the following steps:

1. Copy the contents of your reply from this answer (you can edit this answer (Ctrl/Cmd + click the link to open it in a new tab) and do a Select All -> Copy there).
2. Click on Add Comment on zx8754's post here: A: genotype format with 1 to 4
3. Paste the copied text
4. Click on the green Add Comment button
5. Click on moderate back in your answer here: A: genotype format with 1 to 4
6. Choose Delete Post
7. Click on the blue Submit button.

Thank you!