Question: Trouble Using Bcf Tools.
0
Patrick Leahy • 10 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
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modified 5.6 years ago
by
Jennifer Hillman Jackson ♦ 25k
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written
5.6 years ago by
Patrick Leahy • 10
