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.
Jen Galaxy team
On 3/14/12 5:31 AM, Geert Vandeweyer wrote:
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 ___________________________________________________________ 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:
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