Re-coding genotype in JMPG yields incomplete output dataset

Question

Hello,

I am trying to re-code a genotype data set (~ 40 k SNPs) from diploid format (eg A / G, G / C, etc) to numerical format (0, homo; 1, hete; 2, homo). The re-coding looks good, the issue is that my data output Is incomplete (it only contains ~ 29 k SNPs). I am not getting any error or massage indicating what happened with the rest of my markers.

Could you please give me any clue to solve this issue

I am using JMP Genomics 8.2

Thanks

Chris_Kirchberg · Answer

Hi @Fers,

That is currious. I just recoded 295988 SNPs from AA, AB, and BB to 0,1, and 2.  All of the SNPs are there. I am using JMP Genomics 9.0.

Give Support a call or email them at support@jmp.com and ask them what may be the problem.

Best,

Chris