Pretty print to stdout when the -out argument is not passed in

Let me know if this is what you had in mind. Example output (spacing not shown in the comment):

} {
  "variant" : {
    "org.bdgenomics.adam.avro.ADAMVariant" : {
      "contig" : {
        "org.bdgenomics.adam.avro.ADAMContig" : {
          "contigName" : {
            "string" : "chrM"
          },
          "contigLength" : null,
          "contigMD5" : null,
          "referenceURL" : null
        }
      },
      "position" : {
        "long" : 16321
      },
      "referenceAllele" : "T",
      "variantAllele" : "C"
    }
  },
  "variantCallingAnnotations" : null,
  "sampleId" : {
    "string" : "default"
  },
  "sampleDescription" : null,
  "processingDescription" : null,
  "alleles" : [ "Alt", "Alt" ],
  "referenceReadDepth" : null,
  "alternateReadDepth" : null,
  "readDepth" : null,
  "genotypeQuality" : null,
  "genotypeLikelihoods" : [ ],
  "expectedAlleleDosage" : null,
  "readsMappedForwardStrand" : null,
  "splitFromMultiAllelic" : false,
  "isPhased" : null,
  "phaseSetId" : null,
  "phaseQuality" : null
} {