Convert HLA allele to Genepop format

Question

[seta]

Dear all,

I'm trying to used PGDspider tool to convert HLA allele file to Genepop format, however I'm not successful with it. I selected "convert" in file format (input), and "Genepop" for output format. Could you please let me know your way to convert HLA allele to Genepop format or any format acceptable for Arlequin?

Here is my sample HLA allele file:

NA18500 A*33:01 A*74:01 B*58:01 B*78:01 C*07:01 C*16:01
NA18501 A*33:01 A*66:02 B*14:01 B*78:01 C*08:02 C*16:01

Thanks

[Kevin Blighe]

Can you please elaborate on what is genepop format? Have you seen this question on ResearchGate? - https://www.researchgate.net/post/how_to_convert_allele_data_into_arlequin_format

Seems to be a few questions on the topic over at ResearchGate: https://www.researchgate.net/post/How_to_make_input_file_in_arlequin

[seta]

Yes Kevin, I saw those links, I tried the PGDspider, but it didn't work for me. Based on the example of genepop format at here, I manually changed the above format (in the original post) to the below format:

Loc1, Loc2, Loc3, Loc4, Loc5

POP
NA18500,    3301    7401    5801    7801    1601
NA18501,    3301    6602    1401    7801    1601

Please kindly let me know if it's right in your opinion?

[Kevin Blighe]

I see, can you not use sed and other shell commands to do that?

[seta]

yes, I can use it. But, I just want to make sure this conversion is right?

[Kevin Blighe]

If it is right in which sense? If the program accepts it, then sure. I am not too familiar with the program, to be honest. These genetics programs, I find, suffer from lack of documentation and go out of maintenance quite quickly. One exception is PLINK.