Hello Mahtab,
Some vcftools are in development status on our test server under "VCF Tools" at: http://test.g2.bx.psu.edu/
Adding these and others (including the ones you mention) to the Tool Shed is under consideration by the Galaxy team, but a firm timeline is not set at this time. If your interest is in adding these to the Tool Shed, they would welcomed. Another option is to check in with the galaxy-dev@bx.psu.edu development mailing list to see if any other developer/group has something they could submit to the Tool Shed. Please do not cross-post this thread, though, but instead create a brand new message/thread with the relevant details and request (e.g. not a reply with a new subject line or an added email).
Our primary investment at this time has been in the GATK pipeline. There are differences in the way vcftools vs GATK works, so its not an exact 1:1 mapping of functionality, but you may be able obtain the results you need by using the NGS: GATK Tools (beta) variant utilities (CombineVariants, VariantEval, etc).
The GATK tool set is under active development and wrappers for these can be found in both galaxy-central and galaxy-dist at bitbucket in various stages of stability. Where to pull from depends on the tool (the version will be the same for some in both locations, but this can change over time) and your desire/tolerance to work with tools that are undergoing change. http://bitbucket.org/galaxy/galaxy-dist http://bitbucket.org/galaxy/galaxy-central
Hopefully this provides some useful choices,
Jen Galaxy team
On 8/13/12 8:24 PM, Mahtab Mirmomeni wrote:
Hi
I was wondering if there is a wrapper already for vcftools in Galaxy. I want to use the following functionalities of vcftools but I haven't found it in toolshed.
Thanks Mahtab
Comparing
vcf-compare http://vcftools.sourceforge.net/perl_module.html#vcf-compare A.vcf.gz B.vcf.gz C.vcf.gz
Concatenating
vcf-concat http://vcftools.sourceforge.net/perl_module.html#vcf-concat A.vcf.gz B.vcf.gz C.vcf.gz | bgzip -c > out.vcf.gz
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