Hi all! I am new to Galaxy and having issues with FreeBayes. After I run FreeBayes, I have a list of information with #codes, but no actual data to run further analysis with. Might anyone be able to help?
My history is here: Galaxy
I am using this tutorial for reference: Redirecting…
The freebayes output is empty because the bam file that you gave as input to freebayes is empty.
It is empty because of the Samtools view step.
I think in the samtools view step you need to set the setting Exclude reads with any of the following flags set but you have set Require that these flags are set.
Thank you so much! This worked and I greatly appreciate your help!