I would like to add to the vcf file that I obtained with samtools mpileup the field AD. I did the following command:
samtools mpileup -A -d 6000 -B -C 50 -g -f $ref -s $input.bam | bcftools call -mv -Oz -o $output.vcf
In my vcf file I had these informations in the INFO field:
I would like to have also AD field. Can anyone help me? Thank you!!