How can I get Allele Depth of my vcf file ?
I am attempting to get the Allele Depth (AD) from my vcf file.
I got this file from bcftools file using the function:
bcftools view -c -g scaffold_filt_PV003_q10_variant.bcf > scaffold_filt_PV003_q10_variant.vcf
but when I see the vcf generated in the column called format does not appear AD, only appear GT:PL:GQ I do not another alternative way to see Allele Depth.
Thanks in advance