Annovar annotation with refGene Database How to Dismiss Exon number and Gene Symbol from AAchange Column?
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3.7 years ago
mhmtgenc85 ▴ 40

Dear all,

I use annovar annotation with refGene database as gene annotation. In the output column AAchange the format is like this;

GeneSymbol:Transcript:ExonNo:baseChange:AAchange

But I would like this not to include Gene Symbol and Exon No. So is there a way to manipulate this column of the annotation?

Thanks in advance.

annovar refGene database Variant calling AAchange • 1.6k views
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Hi, if you can use bash and awk and your output is always delimiter by ":" and have same position, you can use one-liner like this: echo "GeneSymbol:Transcript:ExonNo:baseChange:AAchange" | awk '{split($1,arr1,":"); print arr1[2]":"arr1[4]":"arr1[5]}'

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Hi, does it work for you? Can I change my comment to an answer?

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