I am annotating some .txt files by Annovar software by this code
nnovar]$ module load annovar/2016Feb01
[cyan01 annovar]$ table_annovar.pl
But I really got confused to do that by awk
for all of my files in the path; Can somebody help me?
Many thanks
EDITED
I found this but not working
module load annovar/20
for file in *.vcf; do
table_annovar.pl example/a.txt humandb/ -buildver hg19 -out file -remove -protocol refGene,cytoBand,exac03,avsnp147,dbnsfp30a -operation gx,r,f,f,f "$f" > "${f%.*}.txt"
done;