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:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
___________________________________________________________
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:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
