add missing annotations to vcf

[cmccabe]

I am using bcftools version 1.3.1 and trying to add undefined annotations to a vcf before using bgzip and tabix.

If I try to run the norm command on the vcf I get:

bcftools norm -m-both -o file.vcf file.vcf.gz
     
[W::vcf_parse] INFO 'RSC1A1,RSC1A1' is not defined in the header, assuming Type=String
     Could not parse the header line: "##INFO=     <ID=RSC1A1,RSC1A1,Number=1,Type=String,Description="Dummy">"

So I use:

# find undefined annotations#
bcftools view -h file.vcf > header.txt
# add undefined to vcf#
bcftools reheader -h header.txt file.vcf > fixed.vcf

I then use bgzip and tabix on the fixed.vcf and rerun the norm command:

 bcftools norm -m-both -o fix.vcf fixed.vcf.gz
     [W::vcf_parse] INFO 'RSC1A1,RSC1A1' is not defined in the header, assuming Type=String
     Could not parse the header line: "##INFO= <ID=RSC1A1,RSC1A1,Number=1,Type=String,Description="Dummy">"
     [E::vcf_parse] Could not add dummy header for INFO 'RSC1A1,RSC1A1'
     [W::vcf_parse] INFO 'RSC1A1,RSC1A1' is not defined in the header, assuming Type=String
     Could not parse the header line: "##INFO=<ID=RSC1A1,RSC1A1,Number=1,Type=String,Description="Dummy">"
     [E::vcf_parse] Could not add dummy header for INFO 'RSC1A1,RSC1A1'
     Lines   total/split/realigned/skipped:	116/4/0/0

It seems the dummy line with the undefined annotation was not added to the vcf, but I am not sure how to fix it. Thank you .

[finswimmer]

Hello,

is a comma really allowed in the ID definition? Maybe with quotes around?

fin swimmer