[galaxy-user] trouble using bcf tools.

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