Hi everyone, I'm Diego. I'm currently working on an IONTorrent PGM, using a custom amplicon panel of 6 genes, scanning a popolation of several hundred samples. I would ask how to generate the input files needed for PLINK from the files that came out from the IonTorrent Server. the PLINK's tutorial talks about the BED file (the only one I got), a BIM file (a MAP file with a row for each SNP), a FAM file(made from a PED file, with a row for each patient), and pop.phe qt.phe (are they mandatory, or usefull only when are rappresented more than 1 population? how can i generate them? just typing?) How can I generate them all? VCFtools seems to be able to generate the PED and MAP files, which I have to edit for fitting in BIM and FAM for PLINK, right? what about the *.phe files?
I hope this is not a re-posted question. thankig you in advance for your support, I hope you have a nice day