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-...@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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___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
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