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?
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written
by
Fatemeh Nabizadeh •
: "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
awk '!(($23=="Benign" || $23=="Likely benign") && ($29=="Benign" || $29=="Likely benign"))'
Thank you, Mr. Lindenbaum
I tried this command
awk '!(($23=="Benign" || $23=="Likely benign") && ($29=="Benign" || $29=="Likely_benign"))' 2-Exonic > 3-NonBenign
But when getting the word count, the results are the same!
1353 2-Exonic 1353 3-NonBenign
Do you know where is the problem?
So, this is my command:
awk -F "\t" '!(($23=="Benign" || $23=="Likely benign") && ($29=="Benign" || $29=="Likely_benign"))' 2-Exonic > 3-NonBenign
Here is the word count of my output file: 692 3-NonBenign
But has Benign and likely benign variants in columns 23 and 29.
chr1 11826630 11826630 C T PASS hom exonic C1orf167 .
nonsynonymous SNV C1orf167:NM_001010881:exon3:c.C787T:p.P263S intergenic AGTRAP;C1orf167 dist=15802;dist=5509 . . exonic ENSG00000215910 . nonsynonymous SNV
ENSG00000215910:ENST00000433342:exon3:c.C1357T:p.P453S Benign . .
. .
This is an example of Benign in column 23, after using the command.
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written
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Fatemeh Nabizadeh •
|| instead of &&. If Benign and Likely Benign do not occur in any other column, you can do inverse grep or print rows that do not contain these strings (sed/awk).
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