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:
So I use:
I then use bgzip and tabix on the fixed.vcf and rerun the norm command:
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 .
If I try to run the norm command on the vcf I get:
Code:
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">"
Code:
# find undefined annotations# bcftools view -h file.vcf > header.txt # add undefined to vcf# bcftools reheader -h header.txt file.vcf > fixed.vcf
Code:
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
Comment