Hello! I am using plink from https://www.cog-genomics.org/plink2/ I would like to extract all genes from chr1 to different gene files (each file is the data of one gene). I write a loop for --from-bp and --to-bp according to the pos of different gene. Each time I run command (for example)
plink --vcf chr1.vcf.gz --keep keep_indv --chr 1 --from-bp 76291501 --to-bp 76294500 --recode A --maf 0.000000001 --geno 0.2 --out chr1_MSH4.
But I found it is too slow. Each time, plink loads all variants and then extract the gene I want. Is there a way to extract all genes at one time and write them into separate files?