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,

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 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

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