Question: VCF filter filters everything; best forum for questions
gravatar for jrberminghamjr
15 months ago by
jrberminghamjr10 wrote:

I have datasets that have been generated by the naive variant caller, and wish to filter them for variants that have a less than 1/10000 chance of being false positive. I used the filtering expression -f "QUAL > 40" but the output is empty. What am I doing wrong, and is this the correct approach to obtain the desired variants?

Also, is Biostars posts the best forum for a newbie to get answers to basic questions such as the one above?

Thank you,

ADD COMMENTlink modified 15 months ago by Jennifer Hillman Jackson25k • written 15 months ago by jrberminghamjr10
gravatar for Jennifer Hillman Jackson
15 months ago by
United States
Jennifer Hillman Jackson25k wrote:


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 ( 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

ADD COMMENTlink written 15 months ago by Jennifer Hillman Jackson25k

Hey Jennifer, How do you convert the QUAL score produced by freebayes to a PHRED score?

Thank you

ADD REPLYlink written 11 months ago by annet.kyomuhangi10

Hi, The values are already Phred +33 scaled.

Galaxy Tutorials:

Next time, please ask new questions as a new post. You can always link in prior posts that add context. Thanks! Jen, Galaxy team

ADD REPLYlink written 11 months ago by Jennifer Hillman Jackson25k
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