<p>Take one VCF file for example,</p>

<pre><code>##fileformat=VCFv4.1
##samtoolsVersion=0.1.16 (r963:234)
##INFO=&lt;ID=DP,Number=1,Type=Integer,Description="Raw read depth"&gt;
##INFO=&lt;ID=AF1,Number=1,Type=Float,Description="Max-likelihood estimate of the site allele frequency of the first ALT allele"&gt;
....
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  SLVi33.16       SLVi33.25       SLVi33.26
chr1    85691   .       C       T       6.26    .       DP=2;AF1=1;CI95=0.3333,1;DP4=0,0,2,0;MQ=40;FQ=-28.9     GT:PL:GQ        0/1:0,0,0:3     1/1:20,3,0:4    1/1:18,3,0:4
chr1    88338   .       G       A       6.95    .       DP=3;AF1=1;CI95=0.1667,1;DP4=0,0,2,1;MQ=30;FQ=-28.1     GT:PL:GQ        0/1:0,0,0:3     0/1:0,0,0:3     1/1:38,9,0:8
</code></pre>

<p>The DP=2 at chr1:85691, however, there are three individuals in the file, why does every individual has genotype? As AF1 means allele frequency of ALT allele, it supposed to be AF1=5/6 at chr1:85691, why it's truely AF1=1? I'm so confused, anybody can help me? Thanks in advance.</p>

<p>DP is just the raw read depth at that position. DP of 2 just means 2 reads out of your 3 individual samples mapped to that position and passes the quality filter. It doesn't say whether it is 2 reads from one of your individual or 2 read from 2 individuals..etc. </p>

<p>AF1 of 1 pretty much just means the 2 reads (2/2) both have a T instead of an C at that position.</p>

<p>Why are you expecting it to be 5/6? Are you trying to compare this to some other data?</p>

<p>edit **</p>

<p>Samtools is really not great at outputting and calculating the genotype field. <a href="/p/12354/">Here</a> is another biostar questions about it.</p>

<p>The PL fields showing 0,0,0 pretty much means there are no reads covering it. It looks like samtools falsely calculates 0,0,0 as heterozygous because the probabilities are similar (all zeroes in this case). </p>