So I have converted the reprt.txt and map.txt files into .lgen formats. But my conversion from .lgen to bed file keeps failing due to memory issue even though I try to run it chromosome wise.
Here are the first few lines of my files:
DGKH413ADHJW:Plink_working dlekshmi$ head HNPGenotypes.lgen 1 HNP_DNA_1 rs1000000 C C 2 HNP_DNA_1 rs1000002 A G DGKH413ADHJW:Plink_working dlekshmi$ head HNPGenotypes.fam 1 HNP_DNA_1 0 0 0 0 2 HNP_DNA_1 0 0 0 0 DGKH413ADHJW:Plink_working dlekshmi$ head HNPGenotypes.map 12 rs1000000 0 126890980 3 rs1000002 0 183635768
I generated the files based on this code:
https://github.com/dhibar/ADNI_Genetics_Convert_to_PLINK according to the presentation: http://www2.warwick.ac.uk/fac/sci/statistics/staff/academic-research/nichols/presentations/ohbm2014/imggen/Hibar_ImgGen-CommonVar_OHBM2014.pdf
There are whole there are 70000SNPs for over 100 samples. So on the whole around 7 million. Any help will be appreciated.