I have a PLINK formatted database (bed/bim/fam files) and corresponding recoded files (hh/ped/map). I am looking for an effective way to extract samples from this database with specific genotypes. I have looked through the PLINK manual and found that I can extract set of samples using "--keep" parameter and extract set of genotypes using "--extract", am wondering if this can be done in a single step using another parameter or tool.
My input is a list of rsIDs and genotypes; I need to get sample ids and genotype as output. INPUT
Sample1 AA Sample5 AA Sample22 AA ...
Is there any option in PLINK to do this or I should use unix 'grep' and/or a custom script to extract data. Suggestions on other computational genomics tools to do similar task is also welcome.