Filter annotated VCF snpEFF
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?
1 answer
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
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