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)