wierd chars found in vcf file
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Entering edit mode
6 days ago

Hi everyone,

I am trying to run funcotator on wes samples. I have funcotator datasources files from gatk cloud. The tool runs fine, but we ended up seeing some %3D, %20 chars in the result vcf file. It seems like the chars are coming from clinvar files. How do I resolve the problem, it would be helpful if someone can provide a solution.

Regards, Manasa

pipeline variant calling gatk • 158 views
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Entering edit mode
6 days ago

those are URL-escaped strings. See https://www.w3schools.com/tags/ref_urlencode.ASP .

%3D is '=', %20 is space . It avoid some conflicts with the standard separators in the VCF.

How do I resolve the problem, it would be helpful if someone can provide a solution.

well that's not a 'problem' but you'll need some programming if you need to unescape those string. Eg. in the shell: https://stackoverflow.com/questions/6250698/how-to-decode-url-encoded-string-in-shell

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