calculated an LD matrix for a locus using plink2

Hi Everyone,

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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