vcftools

[Tony Travis <tony.travis@minke-informatics.co.uk>]

Hi, Andreas.

I need to process .vcf files with thousands of WGS scaffolds in them
instead of just a few chromosomes. The latest version of "vcftools" can
do this, but the version of "vcftools" currently in Bio-Linux 8/Ubuntu
14.04 LTS is quite old:

> root@wildcat:~# apt-cache policy vcftools
> vcftools:
>   Installed: 0.1.11+dfsg-1
>   Candidate: 0.1.11+dfsg-1
>   Version table:
>  *** 0.1.11+dfsg-1 0
>         500 http://gb.archive.ubuntu.com/ubuntu/ trusty/universe amd64 Packages
>         100 /var/lib/dpkg/status
>      0.1.7-1 0
>         500 http://archive.ubuntu.com/ubuntu/ precise/universe amd64 Packages

I noticed that your Debian-Med version is in Ubuntu Xenial/16.04 LTS:

> vcftools:
>   Installed: 0.1.14+dfsg-2
>   Candidate: 0.1.14+dfsg-2
>   Version table:
>  *** 0.1.14+dfsg-2 500
>         500 http://gb.archive.ubuntu.com/ubuntu xenial/universe amd64 Packages
>         100 /var/lib/dpkg/status

So, I downloaded the source under Ubuntu Xenial/16.04 LTS:

> ajt@beluga:~$ lsb_release -d
> Description:	Ubuntu 16.04.1 LTS
> sudo apt-get source vcftools

Then backported it to Bio-Linux 8/Ubuntu 14.04 LTS

> rwt017@wildcat:~$ lsb_release -d
> Description:	Ubuntu 14.04.5 LTS
> apt install dh-autoreconf
> rsync -axP vcftools-0.1.14+dfsg wildcat:
> cd vcftools-0.1.14+dfsg
> dpkg-buildpackage -B
> cd ..
> gdebi vcftools_0.1.14+dfsg-2_amd64.deb

What would be the correct way to update the version of "vcftools" in
Bio-Linux 8/Ubuntu 14.04 LTS?

Thanks,

  Tony.

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