Please can I just ask how to filter SnpEff output for exonic variants only with SnpSift?
I have tried by calling the initial SnpEff job with sequence ontology annotations.
When I then try to filter as per the sequence ontology annotations it fails. When I’ve viewed the SnpEff VCF output, the sequence ontology annotations don’t seem to be present despite selecting this option when running the initial annotation.
Apologies if this is a basic q, very new to bioinformatics
Thank you for your help
do you see SnpEff annotation in Info column of vcf file? It starts with ANN= or EFF=.
You can select exonic variants by intersection of VCF file with BED file containing location of exons or by selection of appropriate annotations using SnpSift Filter. Check SnpEff Eff HTML stats for valid values, such as missense_variant etc. Decide if you want variants in UTRs and non-coding transcripts. The syntax is described in SnpSift Filter. It might look something like: ANN.EFFECT = ‘missense_variant’) | (ANN.EFFECT = ‘synonymous_variant’) etc. Just in case double check filtering with ‘has’ instead of ‘=’. There might be other options.
Hope that helps.
The brackets have wildcard characters, but these were interpreted as format symbols. If you decide to go with SnpSift Filter, just follow example at the bottom of job setup page.