13 months ago by
This is the right place to ask a question about Galaxy tools (usage, troubleshooting, and the like).
Your query is correct, however, the VCF output from the Naive Variant Caller tool inserts a dot
. for calls passing the mapping quality criteria set on the tool form at execution. Click on the "eye" icon for the VCF dataset to view the content. If you want to only retain calls with
QUAL > 40 when using this tool, enter
40 for the mapping quality filtering option on the tool form instead of post-processing the VCF dataset.
Some variant callers produce a QUAL score and some do not. For example, Freebayes will produce a QUAL score in the VCF output.
This addresses part of your question yesterday (https://biostar.usegalaxy.org/p/24570/) about the advantages/disadvantages of using different tools. I'll put more information into that other post today.
Hope this info helps with usage for this particular tool. Jen, Galaxy team