Question: FreeBayes returning an empty table
gravatar for annet.kyomuhangi
11 months ago by
annet.kyomuhangi10 wrote:

Hi there, If I provide Freebayes with quality scores it gives me an empty table. If I don't provide the quality scores it returns a full table. What could be wrong?

Thank you

galaxy variant vcf bam freebayes • 286 views
ADD COMMENTlink modified 11 months ago by Jennifer Hillman Jackson25k • written 11 months ago by annet.kyomuhangi10
gravatar for Jennifer Hillman Jackson
11 months ago by
United States
Jennifer Hillman Jackson25k wrote:


The input for FreeBayes is a mapped BAM dataset. The input to the mapping tool in used upstream (Bowtie2, BWA/MEM) would contain quality scores, even if provided as default values (using a tool like Combine FASTA and QUAL into FASTQ). Perhaps the jobs were not run with a mapped BAM input?

At Galaxy Main, I see at least one successful FreeBayes job in your recent histories. It uses proper inputs and produces the correct output. I wasn't able to find the jobs with this type of input/output.

If you still need help, and are working at Galaxy main, an email can be sent to from your registered account. Include details about the exact history (share link to history) and FreeBayes output dataset numbers that represent this issue. Make sure all inputs/outputs are left undeleted for full review/feedback. Undelete (if just deleted) or reproduce (if permanently deleted). If there is a problem, we'd like to clarify and fix it.

Galaxy tutorials, including those for Variant Analysis:


ADD COMMENTlink modified 11 months ago • written 11 months ago by Jennifer Hillman Jackson25k
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