Why doesn't a set of DNA-Seq BAM files have corresponding variant calls?

There are multiple reasons that could contribute to an instance in which harmonized tumor and normal BAM files for a specific case are available but the variant calls are not. The two most common reasons are as follows:

1. The variant calling step may not be completed yet.  The GDC may release harmonized alignments before variant calling is completed.
2. One of the BAM files may contain high levels of cross-patient contamination.  This value can be retrieved from the "contamination" field of the file's metadata.  If the value is above 0.04, the variants that originate from the BAM file will not be available.  

See the Data Quality page for more information about how the GDC maintains high-quality data at a large scale.