##GATKCommandLine.GenotypeGVCFs=<ID=GenotypeGVCFs,Version=3.8-1-0-gf15c1c3ef,Date="Fri Jan 31 20:08:34 EST 2020",Epoch=1580519314018,CommandLineOptions="analysis_type=GenotypeGVCFs input_file=[] showFullBamList=false read_buffer_size=null read_filter=[BadCigar, NotPrimaryAlignment] disable_read_filter=[] intervals=[chr1:1-248956422] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/n/app/bcbio/dev/genomes/Hsapiens/hg38/seq/hg38.fa nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=1000 baq=OFF baqGapOpenPenalty=40.0 refactor_NDN_cigar_string=false fix_misencoded_quality_scores=false allow_potentially_misencoded_quality_scores=false useOriginalQualities=false defaultBaseQualities=-1 performanceLog=null BQSR=null quantize_quals=0 static_quantized_quals=null round_down_quantized=false disable_indel_quals=false emit_original_quals=false preserve_qscores_less_than=6 globalQScorePrior=-1.0 secondsBetweenProgressUpdates=10 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=LENIENT_VCF_PROCESSING use_jdk_deflater=false use_jdk_inflater=false disable_auto_index_creation_and_locking_when_reading_rods=false no_cmdline_in_header=false sites_only=false never_trim_vcf_format_field=false bcf=false bam_compression=null simplifyBAM=false disable_bam_indexing=false generate_md5=false num_threads=1 num_cpu_threads_per_data_thread=1 num_io_threads=0 monitorThreadEfficiency=false num_bam_file_handles=null read_group_black_list=null pedigree=[] pedigreeString=[] pedigreeValidationType=STRICT allow_intervals_with_unindexed_bam=false generateShadowBCF=false variant_index_type=DYNAMIC_SEEK variant_index_parameter=-1 reference_window_stop=0 phone_home= gatk_key=null tag=NA logging_level=INFO log_to_file=null help=false version=false variant=[(RodBindingCollection [(RodBinding name=variant source=/n/scratch2/hsph_bioinformatic_core/sn240/atanasova2020/atanasova/work/variation/rnaseq/gatk-haplotype/S10-gatk-haplotype.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant2 source=/n/scratch2/hsph_bioinformatic_core/sn240/atanasova2020/atanasova/work/variation/rnaseq/gatk-haplotype/S11-gatk-haplotype.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant3 source=/n/scratch2/hsph_bioinformatic_core/sn240/atanasova2020/atanasova/work/variation/rnaseq/gatk-haplotype/S12-gatk-haplotype.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant4 source=/n/scratch2/hsph_bioinformatic_core/sn240/atanasova2020/atanasova/work/variation/rnaseq/gatk-haplotype/S13-gatk-haplotype.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant5 source=/n/scratch2/hsph_bioinformatic_core/sn240/atanasova2020/atanasova/work/variation/rnaseq/gatk-haplotype/S14-gatk-haplotype.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant6 source=/n/scratch2/hsph_bioinformatic_core/sn240/atanasova2020/atanasova/work/variation/rnaseq/gatk-haplotype/S15-gatk-haplotype.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant7 source=/n/scratch2/hsph_bioinformatic_core/sn240/atanasova2020/atanasova/work/variation/rnaseq/gatk-haplotype/S16-gatk-haplotype.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant8 source=/n/scratch2/hsph_bioinformatic_core/sn240/atanasova2020/atanasova/work/variation/rnaseq/gatk-haplotype/S17-gatk-haplotype.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant9 source=/n/scratch2/hsph_bioinformatic_core/sn240/atanasova2020/atanasova/work/variation/rnaseq/gatk-haplotype/S18-gatk-haplotype.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant10 source=/n/scratch2/hsph_bioinformatic_core/sn240/atanasova2020/atanasova/work/variation/rnaseq/gatk-haplotype/S19-gatk-haplotype.vcf.gz)]), (RodBindingCollection [(RodBinding name=variant11 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sample_ploidy=2 annotation=[] group=[StandardAnnotation] dbsnp=(RodBinding name=dbsnp source=/n/app/bcbio/dev/genomes/Hsapiens/hg38/variation/dbsnp-151.vcf.gz) filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">