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Question: FreeBayes returning an empty table
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gravatar for annet.kyomuhangi
11 months ago by
annet.kyomuhangi • 10
annet.kyomuhangi • 10 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
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modified 11 months ago by Jennifer Hillman Jackson ♦ 25k • written 11 months ago by annet.kyomuhangi • 10
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gravatar for Jennifer Hillman Jackson
11 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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 https://usegalaxy.org, 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 galaxy-bugs@lists.galaxyproject.org 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: https://galaxyproject.org/learn/

Thanks!
ADD COMMENT • link modified 11 months ago • written 11 months ago by Jennifer Hillman Jackson ♦ 25k
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