Annovar annotation with refGene Database How to Dismiss Exon number and Gene Symbol from AAchange Column?
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.
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Clark_BioMorgan •
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Clark_BioMorgan •
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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]}'Hi, does it work for you? Can I change my comment to an answer?