extract SNPs from compressed PLINK files

Question

[NB]

Hello,

I have a large imputed data set, each file, divided by chromosome and I have a list of 58K SNPs to extract from the imputed data. I managed to convert the imputed data to PLINK format but the output is compressed (ie, map.gz ped.gz). The files are way too large and also time consuming to uncompress it, use PLINK to extract the SNPs and then compress the files again.

Is there any way or any tool that can handle compressed plink files? (tried PLINK already, it doesn't accept compressed files)

Thank you.

[chrchang523]

Is there any reason you can't just decompress them once, and then convert to PLINK binary format (.bed/.bim/.fam), which is simultaneously more compact and much faster to work with?

[NB]

Yes, I would do that if there is no solution as such, it would just take consume a lot of space (and time) on the server which is already limited and the files are too big to transfer it locally on the Desktop...