Hi Mike,
Yes, there is DP and AF under INFO entry. The thing is, it reports only the variants, I don't know if that would be an issue for MixviR, because the GATK command for variant calling reports all the positions.
Here's how it looks like:
#CHROM POS ID REF ALT QUAL FILTER INFO
KX778101.1 289 . T A 18100 PASS DP=3376;AF=0.493187;SB=14;DP4=530,612,907,892
KX778101.1 382 . G A 5753 PASS DP=3314;AF=0.253470;SB=6;DP4=1185,1210,407,457
KX778101.1 785 . C T 4924 PASS DP=3230;AF=0.274613;SB=7;DP4=1106,1154,419,487
Thank you
Leonardo