How can I Converting illumina raw genotype data into PLINK PED format

Question

[mohamadi_yahya]

Hello

The below structure is part of Genotype my data that I would like to convert to plink,

Body Num       ID- Num                          Genotype SNP
704USAHOL    HOLUSAM000069258330          A    A
704USAHOL    HOLUSAM000069258330          A    B
704USAHOL    HOLUSAM000069258330          A    A
704USAHOL    HOLUSAM000069258330           A    B
704USAHOL    HOLUSAM000069258330           A    B

I have 305 separated file that I am going to:

1- Into a single file for format plink

Answer 1

[akang]

You can use GenomeStudio that comes along with illumina data. Ask them to provide it to you in case you don't have it already. It create files ready for Plink. Plink can also read the long format. Check with the plink manual.