Hi there, I have annotated .vcf and .txt file as a result of variant calling pipeline for whole exome sequencing. Now I want to extract almost 50 genes data from these files, either .vcf or .txt.
I used grep command with for loop but it is also extracting the other genes data as well. For example if I want to see only CCL2, grep command is extracting CCL20, CCL28 and so on as well.
i used the following command:
for GENE in `cat Genelist`;
do
grep -i "${GENE}" /Final_annotated_files/1st-Priority/file_name.txt > /Final_annotated_files/1st-Priority/file_output-${GENE}.csv
done
If I used -x instead of -i, loop don't work.
Please help me with the any command which I can used in loops because I have many samples and from each sample I need to extract almost 100 gene's data.
Thanks
1 answer
grep -F -w '${GENE}' in.txt
show us such line+keyword.
Also, check there is no empty line in your Genelist.
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