I have a genotype file in .pgen format, that I subset and would like to calculate LD Matrix for.
Previously I used a .bed file format and use plink 1.9 which worked as charm. But unfortunately my file is in Pgen format which is not supported in plink 1.9 and I have to used version 2.00a3 which support this format. unfortunately I am not able to find any right command to do so.
Any help is appreciated.
command in Plink version 1.9
plink -bfile $maintrLdDir$Probe_c –r2 –out $maintrLdDir$Probe_c –matrix
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