Could you elaborate your question more? Which data and what is the issue?
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I am working on WES data. I have a filtered VCF file that I put into SnpEff on the RAP for annotation. SNP label's a variant as potenitally having 'Loss of Function' effect according to these criteria:
However, I am finding that certain variants that SNP labels as falling under the criteria to be LOF are not being labelled as such. For example: A variant that introduces a stop codon being identified as 'HIGH' impact and as a 'stop_gained' mutation but not being labelled as LOF. I am unsure why this is, and if there is some underlying logic I am unaware of, or if the LOF labelling of SnpEff is not ideal?
My best guess is inherited limited annotation for each DB. If you are open to try out others and integrated annotation, @Ben Busby? has some resource that you can get started.
It is a framework collecting many variant annotation tools and also it has a nice SQL friendly querying language. I would give it an attempt via JupyterLab or ttyd. It pretty configurable and you can download latest annotation databases (which may overcome the issue you observed).
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Could you elaborate your question more? Which data and what is the issue?
I am working on WES data. I have a filtered VCF file that I put into SnpEff on the RAP for annotation. SNP label's a variant as potenitally having 'Loss of Function' effect according to these criteria:
https://pcingola.github.io/SnpEff/se_inputoutput/#loss-of-function-lof-and-nonsense-mediated-decay-nmd-predictions
However, I am finding that certain variants that SNP labels as falling under the criteria to be LOF are not being labelled as such. For example: A variant that introduces a stop codon being identified as 'HIGH' impact and as a 'stop_gained' mutation but not being labelled as LOF. I am unsure why this is, and if there is some underlying logic I am unaware of, or if the LOF labelling of SnpEff is not ideal?
My best guess is inherited limited annotation for each DB. If you are open to try out others and integrated annotation, @Ben Busby? has some resource that you can get started.
Downloading/Accessing a different DB for SNPeff would be a good idea.
In the past, when I worked with VCF annotation tools, I used GEMINI a lot: https://gemini.readthedocs.io/en/latest/
It is a framework collecting many variant annotation tools and also it has a nice SQL friendly querying language. I would give it an attempt via JupyterLab or ttyd. It pretty configurable and you can download latest annotation databases (which may overcome the issue you observed).
I also like wANNOVAR: https://wannovar.wglab.org/tutorial.html
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