Unrecognized problem in a VCF file
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Entering edit mode
5 weeks ago
langzvi • 0

Hi.
I followed the VCF4.2 specification, and created a file in the following structure:

##fileformat=VCFv4.2
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
1   116244010   .   T   C   137.0   .   CO=68
1   116311066   .   G   A   172.0   .   CO=83
1   156100548   .   G   A   115.0   .   CO=51


The file is uploaded to a platform where it gets annotated. I don't know what program or script are used for the annotations, because I can't access them.

The error message I get is the following:

"Annotation failed with the following message: Incorrect header - Some of the VCF header columns are missing".

Can anyone see what may cause the problem with the above structure?

Thanks!

UPDATE
I edited the file according to the comment, yet the error still appears. Now the file looks as follows:

##fileformat=VCFv4.2
##INFO=<ID=CO,Number=1,Type=Integer,Description="Coverage">
#CHROM  POS ID  REF ALT QUAL    FILTER  INFO
1   116244010   .   T   C   137.0   .   CO=68
1   116311066   .   G   A   172.0   .   CO=83
1   156100548   .   G   A   115.0   .   CO=51

vcf • 174 views
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Entering edit mode

I followed the VCF4.2 specification

but I cannot see a definition for INFO/CO ##INFO=<ID=CO,...

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Entering edit mode

Thanks. Is it mandatory to have data in the INFO column? I couldn't find it in the specification. At first it was empty in the VCF file, and that also caused error, so I added the "CO" data. Obviously, it didn't help. Maybe if I'll add what you mentioned.
Also, I checked the file with vcf-validator and got no errors.