Filter annotated VCF snpEFF
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Entering edit mode
5.3 years ago
hkam ▴ 10

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?

snpeff snpsift vcf filter SNP • 4.0k views
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1
Entering edit mode
5.3 years ago

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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