QUAL data is missing in the annotated vcf file.
medaka_haploid_variant reads.fasta ref.fasta -t 30
output : consensus_to_ref.vcf
It has no annotations. So I annotated the vcf
medaka tools annotate consensus_to_ref.vcf ref.fasta mapped-sorted.bam variants.annot.vcf
In this vcf, there is no information in the 'QUAL' column
Am I doing something wrong?