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Monday, May 20, 2013

How to Install Vcftools

Vcftools is a handy program to manipulate .vcf files.  This page describes how to install vcftools.  Here is a brief summary of what to do.

1) Download the most recent version of vcftools.
2) Extract vcftools using the extract command or the following line of code.

3) To build vcftools, cd into the vcftools directory and type make.
4) Add the following two lines to you .bashrc file and then type source .bashrc.

One final note: vcftools requires .vcf files be zipped by bgzip and indexed by Tabix.  To install Tabix, see these installation instructions.  Enjoy using vcftools!


  1. and then you type "make" and nothing happens.

  2. When you type make, is your current directory the vcftools directory?

  3. typed make in the directory of vcftools and then gave me this

    make: *** No targets specified and no makefile found. Stop.

    please note that I'm trying to install it on my mac ox 10.10.5

  4. I did on my mac too. Once you have the file and you extract it, make sure you chose the extracted file as you directory. Once you do that type make.

    1 cd vcftools_0.1.13
    2 make