Question: Specific versions of samtools and bcftools
0
gravatar for Will
3.4 years ago by
Will4.4k
United States
Will4.4k wrote:

So, I'm trying to figure out how I installed my `samtools` and `bcftools` versions so I can replicate it across different computers using conda. I know I installed it from the "download zipfile" on the website which gives you the most recent master clone. With all of the differences between different versions of samtools outputs and input arguments I can't get it to work with any of the 0.2.0-rc*.

I know my samtools version is 0.1.18 (r982:295) and bcftools is 0.1.17-dev (r973-277). But because of the way the Github repo is setup I can't figure out which git-sha these correspond to.

Does anyone know which versions these might be? Or any way to figure it out?

software • 1.6k views
ADD COMMENTlink written 3.4 years ago by Will4.4k

I may be wrong, but isn't it a version that was hosted on SF like: http://sourceforge.net/p/samtools/code/982/ ?

ADD REPLYlink written 3.4 years ago by Pierre Lindenbaum102k

That solves the samtools problem. But it doesn't seem to work for the bcftools. There's a sourceforge page for vcftools (http://sourceforge.net/projects/vcftools/) and that only goes to release 972

ADD REPLYlink written 3.4 years ago by Will4.4k

bcftools 0.1.17-dev (r973-277) came with samtools 0.1.18, it wasn't part of vcftools.

[dpryan@DustPuppy bcftools]$ pwd
/Users/dpryan/Downloads/samtools-0.1.18/bcftools
[dpryan@DustPuppy bcftools]$ ./bcftools

Program: bcftools (Tools for data in the VCF/BCF formats)
Version: 0.1.17-dev (r973:277)
ADD REPLYlink modified 3.4 years ago • written 3.4 years ago by Devon Ryan73k
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