Hello Patrick, MPileup was run with the option to output a "pileup" dataset, not a "bcf" dataset. To change the output type, alter the MPileup form setting " Genotype Likelihood Computation" to be " Perform genotype likelihood computation". Hopefully this helps, Jen Galaxy team On 4/18/13 8:28 AM, Patrick Leahy wrote:
Dear galaxy help, Devon
new user making good headway on galaxy cloud here at Case Western Reserve university in Cleveland Ohio.
I have a small project. 10 human samples. I did a custom capture of exons from 171 genes. Total target size is ~ 0.5 Gb. PE reads from Illumina HighScan.
See attached screenshots. I uploaded one fastq file (1.2Gb).
I succeeded in doing fastQC, groomer, trimmer, allignment with Bowtie, SAM to BAM, mpileup. Now, I want to convert to .vcf. for downstream work.
I got stuck at bcf tools ( see second slide). It is as if bcf tools doesn't recognize the output from mpileup. Note how the option windows in bcf tools are all collapsed.
I used default parameters throughout the workflow. Any Ideas. Patrick
-- Patrick Leahy, Ph.D. *Asst. Professor, General Medical Sciences- Oncology* Scientific Coordinator, Integrated Genomics Shared Resource (IGSR) Scientific Managing Director Microarray Core Facility Director, Laser Capture Microdissection Service Case Western Reserve University Room 3541 Wolstein Research Building 2103 Cornell Rd Cleveland, OH 44106 t: 216 368 0761 f: 216 368 8919 http://cancer.case.edu/members/gms_onc/leahy.html
___________________________________________________________ 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, please use the interface at:
To search Galaxy mailing lists use the unified search at:
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org