From Genome Analysis Wiki
==== Specifying Discard Rules ====
When specifying the discard rules, you should use the constants found at the top of VcfFileReader.h
and discards reads that do not have <code>PASS</code> in the <code>FILTER</code> field and reads that have a genotype that is not phased or have no <code>GT</code> in the <code>FORMAT</code> fields.
==== Read only Certain Sections of the File / Using a VCF Index (TABIX) File ====