Filtering specific genes
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6.4 years ago
basalganglia ▴ 40

Hi helpful bioinformaticians ,

I want to filtering specific gene from my vcf file using SnpSift and my command is ,

 

java -jar SnpSift.jar filter "ANN[*].GENE = 'gene')" a.vcf > b.vcf

 

But I got response as ;

 

line 1:19 no viable alternative at input '[*].GENE=gene)'

What I should do?

Many thanks,

BG

snpsift gene filter • 1.3k views
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Entering edit mode

Hi,

Was there an answer to this because I am too having the same issues "ANN[*].GENE:" is just outputting all the ANN fields and not the gene name specifically.

Thanks, Anj

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