PLINK input file. how convert vcf files (IonTorrent) into it.

Question

[IndyDNA]

Hi everyone,

I'm Diego. I'm currently working on an IONTorrent PGM, using a custom amplicon panel of 6 genes, scanning a population 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 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 useful 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. Thank you in advance for your support, I hope you have a nice day

Diego

Answer 1

[christopher medway]

.map and .ped are a great start. You can convert .map and .ped into the binary format (.bim .bed .fam) in PLINK using the --recode --make-bed command. Note that the binary files offer no new information compared to .map and .ped - they are just a more efficient format for whole-genome data.