Public servers often have limits applied to max read depth due to the computational resources available at that server.
- Mpileup max read depth = 1024
- Varscan max read depth = 200
- Freebayes max read depth = default is to evaluate “all best alleles”
If you should decide to use Freebayes instead, review the pre-sets under the form option: Choose parameter selection level. Each “pre-set parameter” choice is described in the tool form. The “full parameter” choice allows you to tune all settings on your own. If you pick your own settings, be aware that this can create a job that is too large and may fail for resource reasons.
- See the Freebayes manual for help with what each parameter is doing. Example: GitHub - freebayes/freebayes: Bayesian haplotype-based genetic polymorphism discovery and genotyping.
- Galaxy Variant analysis tutorials: Galaxy Training!
Help for jobs that run out of resources at public Galaxy servers, including how to set up your own Galaxy where you can control the resources. Note: allocating more resources won’t solve all “resource” failures as tools have native limits (whether used in Galaxy or not).