Hi, my goal is to make a vcf file combining 30 samples. I have trimmed all 30 samples, converted them into sam/bam files, and sorted, all separately. Then I combined them, with the reference genome, to form a bcf then vcf file. Then I realize that the QUAL value of every line is low (prob all 0).
My question: which step did I do wrong, or this is normal, or this is only the problem of the samples?
Here is what I got: