Having issue with exome sequencing - Deprecated tool (BWA for Illumina) in older workflow



I uploaded my forward and reverse , I selected the hg19 and used bwa for short read to map . I get this error

Could not display BAM file, error was:
file has no sequences defined (mode=‘rb’) - is it SAM/BAM format? Consider opening with check_sq=False

I am trying to follow this pipeline


Hi - This workflow is over 5 years old (from 2014) and most of the tools included now have newer versions and should be updated in the workflow before use. In particular, the BWA for Illumia tool has been deprecated and can produce unexpected results/errors. It seems like you are not getting any hits.

Either BWA or BWA-MEM are a better choices for mapping. If you do not get hits again, you’ll need to check your inputs and tool settings.

FAQs: https://galaxyproject.org/support/#troubleshooting

The Galaxy tutorials include updated tools/methods/workflows. You will probably want to review those in the category Variant Analysis.


Hi Jennifer,

I heard that BWA-MEM is not for short reads like WES, but for WRS !
however, I did selected the BWA as you suggested and it seems like mapped some for me.
is there a possibility to show me how to selected the variant calling as shown here https://galaxyproject.github.io/training-material/topics/variant-analysis/tutorials/exome-seq/tutorial.html I want to use all algorithms you have mentioned here

Thanks a bunch


To use all of the tools in the Exome-seq tutorial, use the Galaxy EU aka “Galaxy Europe” public server at https://usegalaxy.eu. Search for tools at the top of the tool panel.

Screenshot of Galaxy public server choices:

Screenshot of tool panel search function: