Silly question time: I have been using Freebayes to find variants in my data, using the simple setting with filtering. When setting the min coverage level i have been using 10. thinking this meant that it needed a minimum of 10 total reads to evaluate the site for a SNP. However some of the out put variants have DP less than 10... so what does coverage actually mean in this case please?
thanks
Hello,
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
Thanks Jen, Thats very helpful. Is there a glossary somewhere on galaxy for terms like this, as they don't always mean what you think they mean and it would be really helpful for a novice like me.
Galaxy doesn't create distinct documentation for tool options apart from the notes and links on tool forms. For Freebayes and most 3rd party tools, the manual for the wrapped tool (along with any related publications, forums, blogs, etc) is the best way to learn about parameters usage/combinations. Some tools are included in tutorials where the options utilized are discussed with respect to that particular analysis example.
We do have an FAQ that lists out many common datatypes with some having format details and other resources through links. These often will point to the format specification and/or the datatype creator's documentation. For example, VCF format is covered here: https://galaxyproject.org/learn/datatypes/#vcf
