Entering edit mode
6.4 years ago
ambi1999 ▴ 50
The QUAL field in vcf output of Naive Variant Caller is empty for all the variants. Any reason? Attached is screenshot of the vcf.
A related question: Running ANNOVAR Annotate VCF with the above vcf is empty. Not sure if it is realted to QUAL being empty in the vcf but just thought the ask.
Based on this screenshot not a single individual carries one of those variants, which I would guess leads to absence of quality score of said variant (all are 0/0). But I'm unfamiliar with naive variant caller so perhaps my answer is overly naive.
... that screen... is... is it ... is it ... is it Microsoft Excel... ? :-)
Certainly looks like it, call the excellcorcist. I will prepare the holy water.
yes, screen shot is of excel. Opened vcf in a text editor and pasted in excel to display fields properly.
Just updated the image to include some variants where AC is more than 0.
Right, so my hypothesis doesn't fit this new data.
Based on something I found online the output examples also don't have quality scores.
It appears that your post has been cross-posted to another site: http://biology.stackexchange.com/questions/53561/empty-qual-filed-in-naive-variant-caller-vcf-output
This is typically not recommended as it runs the risk of annoying people in both communities.