From Genome Analysis Wiki
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.
Additional Rules =====
There are additional discard rules that can be specified by calling methods on VcfFileReader.
VcfSubsetSamples* subset</code> parameter is a pointer to the subset of samples that you want to include when counting the number of alternate alleles . If all samples that are read/kept are to be included, NULL should be passed in.
minAltAlleleCount</code> parameter is the minimum number of alternate alleles found in the subset in order for the record to be kept.
Use the following method to remove the DiscardMinAltAlleleCount rule: