I was wondering if there is a wrapper already for vcftools in Galaxy.
want to use the following functionalities of vcftools but I haven't
it in toolshed.
vcf-compare <http: vcftools.sourceforge.net="" perl_module.html#vcf-="" compare="">
vcf-concat <http: vcftools.sourceforge.net="" perl_module.html#vcf-="" concat="">
B.vcf.gz C.vcf.gz | bgzip -c > out.vcf.gz
Some vcftools are in development status on our test server under "VCF
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
email@example.com development mailing list to see if any other
developer/group has something they could submit to the Tool Shed.
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.
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
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
be found in both galaxy-central and galaxy-dist at bitbucket in
stages of stability. Where to pull from depends on the tool (the
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
Hopefully this provides some useful choices,