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Convert HLA allele to Genepop format

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

pgdspider genepop
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updated by Ram Ram • written by seta 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?

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written by seta seta

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

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written by Kevin Blighe Kevin Blighe

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

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written by seta seta

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.

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written by Kevin Blighe Kevin Blighe

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