Transcript Based Annotation of Variants Using Annovar

Question

[hkarakurt]

Hello everyone, I am using Annovar for variant annotation but as you may know Annovar outputs shows all possible transcripts in a single line such as:

SMPD1:NM_000543:exon3:c.1148A>G:p.N383S,SMPD1:NM_001318087:exon3:c.1148A>G:p.N383S,SMPD1:NM_001318088:exon3:c.227A>G:p.N76S,SMPD1:NM_001007593:exon3:c.1145A>G:p.N382S

Is it possible to annotate variants for each transcript such as:

SMPD1:NM_000543:exon3:c.1148A>G:p.N383S
SMPD1:NM_001318087:exon3:c.1148A>G:p.N383S
SMPD1:NM_001318088:exon3:c.227A>G:p.N76S
SMPD1:NM_001007593:exon3:c.1145A>G:p.N382S

All other columns such as frequency will remain same. We are not using canonical transcripts for each sample and having all possible transcripts in a single row causes some mistakes. An Annovar option or another tool would be a nice solution if there is.

Thank you in advance.

Answer 1

[young_bioinformatician]

Hi,

you can basically use sed command in bash.

sed 's/,/\n/g' your_annovar_file > your_new_annovar_file

This command transfers the changes in the existing file to the new file. So your previous file still exists.

PS. I just modified my answer based on GenoMax suggestion. Thank you for the warning !

the old version

sed '-i s/,/\n/g' your_annovar_file

This command makes changes to the existing file.

[GenoMax]

Be careful about recommending the -i option which edits file in place. It may mess up the file and need someone to repeat the analysis again. In this case making a separate file would be the prudent choice.

[hkarakurt]

Thank you for your answer. Actually, my mistake, I did not mention some details. Annovar output is a CSV file and it has multiple columns. I want to modify base on only one column in this case

[bk11]

You can extract the the column you want from csv file of your annovar result and have them in separate lines for each transcript as follows-

awk -F"," '{print $YOUR_COLUMN}' your_new_annovar_file.csv | sed 's/,/\n/g' >your_result_file