Filter annotated VCF snpEFF

Question

[hkam]

So I am completely new to this..

I have annotated a cancer VCF file (containing parental and drug resistant cell line) in snpEFF, and now I want to view only the mutations that are in exons (my current file shows all predicted mutations).

What can I use to make a file including only exons/protein-coding regions, please?

Is there a snpSift command that can be used?

Answer 1

[Nicola Casiraghi]

I think that what are looking for is well documented here: http://snpeff.sourceforge.net/SnpSift.html#filter

Take a close look at paragraphs SnpEff 'ANN' fields and SnpEff 'EFF fields