In Vcf file, generate by samtools mpileup, there is an AD field (Allelic depth). This field is suppose to replace the previous DP4 field (Number of high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases).
But when I use -t DP4, AD in mpileup, I have a different number of values in the 2 fields:
And I don't understand why one data is missing in the AD field... Is it not supposed to be like the DP4, so:
high-quality ref-forward, ref-reverse, alt-forward and alt-reverse bases
After that I am not sure: what there are 3 values in the AD field ? And what are the differences between AD and DP4?
Thanks for your help.