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Annovar - Annotated file cells show string

Hello, I am new to bioinformatics and trying to get annovar to work. I was able to download the databases and get annovar working with the example files.

But when I try to use VCF files, the annotated file's cells have a descriptive string along with the actual score or allele frequency. Like this "ClinPred_pred=." Please check the image below. how my output file cells look

This happens with the ex2.vcf example file provided by annovar too, and also even if I convert my vcf to avinput first and try. It works normally with the ex1.avinput file though.

Since these cells are not numbers, I am unable to filter or sort it with excel. So I was wondering if I am missing something. What is the use of this? How do I remove this and should I remove it? Any help would be great. Thanks, Roshan

annovar
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written by Roshan • Roshan

'.' means the value is unknown.

use bcftools , awk, etc.. to filter vcf files, do not use excel.

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written by Pierre Lindenbaum Pierre Lindenbaum

Hi Pierre, thanks a lot for your reply. I am getting started with bioinformatics and not well versed with bcftools to use it. I have previously used VCF files with excel to filter and they didnot have this string in the cells. Even the example avinput file doesnot produce such results after annotation. I will surely try to get better at bioinformatics and learn how to filter with these. Meanwhile is there a way to remove these.

Thanks again, Roshan

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written by Roshan • Roshan

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