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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!
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6 comments:

  1. InigoApril 18, 2014 at 4:10 PM

    and then you type "make" and nothing happens.

    ReplyDelete
  2. AdminApril 18, 2014 at 10:42 PM

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

    ReplyDelete
  3. UnknownNovember 4, 2016 at 9:47 AM

    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

    ReplyDelete
  4. UnknownJuly 26, 2017 at 11:10 AM

    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

    ReplyDelete
  5. UnknownJuly 19, 2020 at 3:21 AM

    Johnpaul@JP /
    $ ls
    '~' dev tmp
    bin etc usr
    cygdrive home var
    Cygwin.bat lib vcftools_0.1.13.tar.gz
    Cygwin.ico proc vcftools-vcftools-581c231
    Cygwin-Terminal.ico sbin vcftools-vcftools-v0.1.16-18-g581c231.tar.gz

    Johnpaul@JP /
    $ cd vcftools-vcftools-581c231

    Johnpaul@JP /vcftools-vcftools-581c231
    $ make
    -bash: make: command not found

    ReplyDelete
  6. UnknownJuly 19, 2020 at 3:23 AM

    why not type in every step in your terminal the copy and paste so that newbies will follow the exact command you are typing in

    ReplyDelete

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