VCFtools installation and versions

Question

[remi.b.md]

I am trying to install vcftools on MAC OS X 10.11.3.

I first installed it with homebrew

brew install vcftools

but when I do man vcftools, it appears the version that has been installed is v0.1.13 while I was expecting the version 4.1 or something similar from what I could read online.

So, following the README.md, I tried via git and I got stuck at

$ ./autogen.sh
./autogen.sh: line 3: autoreconf: command not found

I tried via the tar release downloaded from the left column here and I got stuck at the following errors

$ ./configure
./configure: No such file or directory
$ ./configure.ac
./configure.ac: Permission denied

Did homebrew install the most recent version or is the version that homebrew install by default outdated?

If my version is outdated, can you please help me out to install a new version?

Answer 1

[igor]

The latest version is 0.1.14. Listed at https://github.com/vcftools/vcftools/releases and https://vcftools.github.io/man_latest.html

On their website, it says "VCFtools is compatible with VCF versions 4.0, 4.1 and 4.2". That's probably where you got confused. Those are versions of the VCF file format.

[remi.b.md]

Indeed that's what raised my confusion. Also the fact that a version starting with a zero often mean that the produce is unfinished and not ready to be distributed contributed to my confusion. Thank you!

[igor]

I feel like version 0 doesn't mean much in bioinformatics. Many version 0 tools were very stable (Bowtie, BWA, samtools, just to name a few). On the other hand, there are many that are past 1 that have very obvious problems.