I'm using this command line:
samtools mpileup SAMPLE.bam -f GENOME.fasta -B -d 1000 -R -Q 20 -l BEDFILE.bed -t ADF,ADR,SP,INFO/AD,INFO/ADF,INFO/ADR -v > OUTPUT.vcf
and the resulting VCF lines look pretty much like this:
chr2 70000005 . T G,<*> 0 . DP=64;ADF=29,0,0;ADR=23,3,0;AD=52,3,0;I16=29,23,0,3,1942,74680,82,2354,3060,183600,180,10800,1072,25682,60,1350;QS=0.958481,0.041519,0;VDB=0.148533;SGB=-0.511536;RPB=0.289223;MQB=0.998456;MQSB=0.970565;BQB=0.0683671;MQ0F=0.03125 PL:SP:ADF:ADR 0,88,255,157,255,255:10:29,0,0:23,3,0
which is different from a "typical" VCF line (example taken from the internet):
chr10 3360 . T C 103 . DP=31;AF1=0.5;CI95=0.5,0.5;DP4=6,3,13,9;MQ=20;FQ=27;PV4=1,0.13,1,0.015 GT:PL:GQ 0/1:133,0,54:57
In particular I was interested in the AF1 and DP4 information which is not provided.