Entering edit mode
2.4 years 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
but I cannot see a definition for INFO/CO
##INFO=<ID=CO,...
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.