I simulated reads for a list of variant sites using GATK SimulateReadsForVariants tool. From that, I get a bam file output. Next I create a pileup using samtools mpileup.
samtools mpileup -t DP,DPR,DV,INFO/DPR -vuf GRCh37.fa -l snp.file.vcf simreads.bam > simreads.raw.vcf
The problem is that the output is not giving me correct counts at the variant sites. Here's an example of the first two SNP sites from the pileup.
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT NA12878
1 837214 . G <X> 0 . DP=20;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0;DPR=0,0 PL:DP:DV:DPR 0,0,0:0:0:0,0
1 851390 . G <X> 0 . DP=20;I16=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0;QS=0,0;MQ0F=0;DPR=0,0 PL:DP:DV:DPR 0,0,0:0:0:0,0
So why would all the counts (with the exception of the DP tag) be 0? I opened up the bam file in IGV to check the first couple of sites and the reads do pileup there as they should.