Annovar annotation with refGene Database How to Dismiss Exon number and Gene Symbol from AAchange Column?

Question

[Clark_BioMorgan]

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.

[Paul]

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]}'

[Paul]

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