Update VCF format version to 4.2

testdata/picard/vcf/vcfFormatTest.bad_dict.vcf

@@ -1,4 +1,4 @@
-##fileformat=VCFv4.1
+##fileformat=VCFv4.2
 ##ApplyRecalibration="analysis_type=ApplyRecalibration input_file=[] read_buffer_size=null phone_home=NO_ET gatk_key=/humgen/gsa-hpprojects/GATK/data/gatk_user_keys/gsamembers_broadinstitute.org.key read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false input=[(RodBinding name=input source=/broad/hptmp/ami/tmp/CEUTrio_UG_Both_WG/CEUTrio.HiSeq.WGS.b37.listindel.unfiltered.vcf)] recal_file=(RodBinding name=recal_file source=/broad/hptmp/ami/tmp/CEUTrio_UG_Both_WG/CEUTrio.HiSeq.WGS.b37.listindel.recal) tranches_file=/broad/hptmp/ami/tmp/CEUTrio_UG_Both_WG/CEUTrio.HiSeq.WGS.b37.listindel.tranches out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub ts_filter_level=95.0 ignore_filter=null mode=INDEL filter_mismatching_base_and_quals=false"
 ##CombineVariants="analysis_type=CombineVariants input_file=[] read_buffer_size=null phone_home=STANDARD gatk_key=null read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/humgen/gsa-hpprojects/GATK/bundle/current/b37/human_g1k_v37.fasta nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=0 disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 defaultBaseQualities=-1 validation_strictness=SILENT remove_program_records=false keep_program_records=false unsafe=null num_threads=1 num_cpu_threads=null num_io_threads=null num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false logging_level=INFO log_to_file=null help=false variant=[(RodBinding name=variant source=CEUTrio.HiSeq.WGS.b37.listsnp.recalibrated.filtered.vcf), (RodBinding name=variant2 source=CEUTrio.HiSeq.WGS.b37.listindel.recalibrated.filtered.vcf)] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub genotypemergeoption=UNSORTED filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED multipleallelesmergetype=BY_TYPE rod_priority_list=null printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=true minimumN=1 suppressCommandLineHeader=false mergeInfoWithMaxAC=false filter_mismatching_base_and_quals=false"
 ##FILTER=<ID=LowQual,Description="Low quality">