I used medaka_haploid_variant caller to identify variants in my viral reads. After running medaka tools annotate, I got an annotated vcf file. Then filtering by bcftools,
bcftools complaining about GT not defined in the annotated vcf
bcftools filter -Ob -e 'DP<1000' -o filtered.vcf annotated.vcf
I got the following error
FORMAT 'GT' at NC_xxxxx:33 is not defined in the header, assuming Type=String
From the github post I made https://github.com/nanoporetech/medaka/issues/257, I came to that GT does not appear in the VCF header but does occur in the records which is a bug in medaka.
Now, how to run bcftools by ignoring the GT? Is it possible?