20 days ago by
The coverage filter is applied to the number of mapped reads before other filters are applied. If you have applied other filters, these can remove even more reads from the analysis, reducing the final number of reads used to make the call (what is counted in the DP field, per sample).
If you want to only consider calls that have at least 10 contributing reads (after all filters are applied), the DP field can be filtered with the tool NGS: VCF Manipulation > VCFfilter: filter VCF data in a variety of attributes.
When using the pre-set parameters, the settings/filters applied are listed directly on the tool form in the help section. You can tune these yourself by adjusting the settings under Choose parameter selection level > 5. Full list of options. All are annotated with the command-line option and can be directly compared to the Freebayes documentation to learn more about what each actually does.
Galaxy tutorials, including those for variant analysis that use Freebayes: https://galaxyproject.org/learn/
Thanks! Jen, Galaxy team