Hello Geert,
To produce and work with VCF data, please see the tool groups 'NGS:
Variant Detection' and 'NGS: GATK Tools (beta)'. Each tools has
notations about input, outputs, and sources. We are developing
additional support within Galaxy for these tools as they move out of
beta status. For now, referencing original documentation through the
links on the tool forms to the program source is the best way to learn
more about functionality details.
These are new on the public main server since you originally wrote in,
most are still considered to be 'beta', and implementation feedback is
welcomed. A set of specific 'VCF Tools' are under development to perform
file transformations and other tasks (what your original question is
requesting), but those available on our test server are not yet
recommended/supported.
Best,
Jen
Galaxy team
On 3/14/12 5:31 AM, Geert Vandeweyer wrote:
Hi,
This might be an easy question, but I can't find the solution in the
standard galaxy tools it seems. How do I create a valid VCF file from a
(filtered) samtools mpileup output?
Thanks in advance !
Geert
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The Galaxy User list should be used for the discussion of
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at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
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