I am trying to filter out the Benign variants from my tsv file and 2 columns are having the verdict of pathogenicity. columns 23 and 29 (InterVar_automated and ClinSig, respectively).
The annotation for column 23 is as follows:
Benign Likely benign Likely pathogenic Pathogenic Uncertain significance
The annotation for column 29 is as follows:
Benign Likely_benign Likely_pathogenic Pathogenic Uncertain_significance
I can not use this command:
grep -iv benign 'fileName_or_filePath'
Because it is possible to miss a variant that is likely_benign based on ClinSig, but is VUS based on InterVar.
I want to use an awk command to say: "I do not need a variant if it is Benign or Likely benign based on column 23, AND also if it is Benign or Likely_benign based on column 29.
How can I do this?