My name is Guilherme and first off all I would like to leave here my excuses for the possible dumb question, because I'm relative new in the Bioinfo. area…..so here's my question......
I would like to know if there is a way to convert the VCF files (I got sequences of a region of interest of Chromossome 6 from the FTP download website of the 1000Genome), to Haploview files, so I can work with the Haploview program. Actually I'm wondering if there is a way to get the 1000Genome sequences directly with the Haploview program like the program does with the HapMap Project website.
I'm not familiar with the VCFtools / tabix …. and I just used these programs to get the sequences from the FTP.
The plink --recodeHV option makes a text-based PED and a .info file that Haploview will read. I've found with vcftools the transposed ped file (--plink-tped) is the only way to gt big regions to work, otherwise vcftools crashes because of memory errors.