##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##GATKCommandLine.VariantAnnotator=<ID=VariantAnnotator,Version=3.6-0-g89b7209,Date="Sat Jan 28 16:26:58 EST 2017",Epoch=1485638818727,CommandLineOptions="analysis_type=VariantAnnotator input_file=[bam/PANVJJ_Normal.realigned.md.bam, bam/PANVJJ_Tumor.realigned.md.bam] showFullBamList=false read_buffer_size=null read_filter=[BadCigar] disable_read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL interval_padding=0 reference_sequence=/data/CCRBioinfo/public/GATK/bundle/2.5/hg19/ucsc.hg19.fasta nonDeterministicRandomSeed=false disableDithering=false maxRuntime=-1 maxRuntimeUnits=MINUTES downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 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 validation_strictness=SILENT remove_program_records=false keep_program_records=false sample_rename_mapping_file=null unsafe=ALL 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=(RodBinding name=variant source=variant/strelka/PANVJJ_Normal_Tumor.strelka.indels.annotated.vcf) snpEffFile=(RodBinding name= source=UNBOUND) dbsnp=(RodBinding name= source=UNBOUND) comp=[] resource=[] out=/gpfs/gsfs2/users/CCRBioinfo/projects/TargetOsteoDiscovery/variant/strelka/PANVJJ_Normal_Tumor.strelka.indels.gatk.annotated.vcf annotation=[AlleleBalanceBySample, MappingQualityZeroBySample, MappingQualityZero, QualByDepth, ReadPosRankSumTest, BaseQualityRankSumTest, HaplotypeScore, RMSMappingQuality, LowMQ, HomopolymerRun, BaseCounts, FisherStrand, SpanningDeletions] excludeAnnotation=[] group=[] expression={} resourceAlleleConcordance=false useAllAnnotations=false list=false alwaysAppendDbsnpId=false MendelViolationGenotypeQualityThreshold=0.0 filter_reads_with_N_cigar=false filter_mismatching_base_and_quals=false filter_bases_not_stored=false">
##SnpEffCmd="SnpEff  -s variant/strelka/PANVJJ_Normal_Tumor.strelka.indels.annotated.snpEff_summary.html GRCh37.75 "
##SnpEffVersion="4.3g (build 2016-11-28 08:31), by Pablo Cingolani"
##SnpSiftCmd="SnpSift annotate -noid -a -info CLNORIGIN,CLNSIG,CLNDSDB,CLNDSDBID,CLNDBN,CLNACC /data/CCRBioinfo/zhujack/Ref/hg19/clinvar_147_GRCh37.p13.vcf /dev/stdin"
##SnpSiftCmd="SnpSift annotate -noid -a -name Cosmic.. -info CosmicID,CNT,SNP /data/CCRBioinfo/zhujack/Ref/hg19/CosmicCodingMuts_grch37_v79.added_CosmicID.added_chr.chrMT2chrM.sorted_header.vcf /dev/stdin"
##SnpSiftCmd="SnpSift annotate -noid -a -name ESP6500.. -info MAF,HGVS_CDNA_VAR /data/CCRBioinfo/zhujack/Ref/hg19/ESP6500SI-V2-SSA137.updatedRsIds.snps_indels.vcf /dev/stdin"
##SnpSiftCmd="SnpSift annotate -noid -a -name ExAC.. -info AF,ESP_AF_GLOBAL,KG_AF_GLOBAL,AC_AFR,AC_AMR,AC_EAS,AC_FIN,AC_NFE,AC_SAS,AC_OTH,AN_AFR,AN_AMR,AN_EAS,AN_FIN,AN_NFE,AN_SAS,AN_OTH /data/CCRBioinfo/zhujack/Ref/hg19/ExAC.r0.3.1.sites.vep.vcf /dev/stdin"
##SnpSiftCmd="SnpSift annotate -noid -a -name dbSNP.. -info CAF,CDA,COMMON,dbSNPBuildID,G5,G5A,GENEINFO,KGPhase1,KGPhase3,MUT,OTH,RS,RSPOS,SAO,SSR,VC,VLD /data/CCRBioinfo/zhujack/source/data/dbsnp_147_GRCh37.p13.added_chr.chrMT2chrM.sorted.header.vcf /dev/stdin"
##SnpSiftCmd="SnpSift dbnsfp -a -f 1000Gp1_AF,1000Gp1_AFR_AF,1000Gp1_AMR_AF,1000Gp1_ASN_AF,1000Gp1_EUR_AF,CADD_phred,CADD_raw,codonpos,Ensembl_geneid,Ensembl_transcriptid,fold-degenerate,genename,Interpro_domain,Polyphen2_HVAR_pred,Polyphen2_HVAR_score,refcodon,SIFT_pred,SIFT_score,Uniprot_acc,Uniprot_id,UniSNP_ids variant/strelka/PANVJJ_Normal_Tumor.strelka.indels.raw.vcf"
##SnpSiftVersion="SnpSift 4.3g (build 2016-11-28 08:32), by Pablo Cingolani"
##cmdline=/usr/local/apps/strelka/1.0.15/libexec/consolidateResults.pl --config=/lscratch/31998040/strelka/config/run.config.ini
##content=strelka somatic indel calls
##fileDate=20170128
##germlineIndelTheta=0.0001
##priorSomaticIndelRate=1e-06
##reference=file:///data/CCRBioinfo/public/GATK/bundle/2.5/hg19/ucsc.hg19.fasta
##source=strelka
##source_version=2.0.17.strelka2
##startTime=Sat Jan 28 16:16:09 2017
##INFO=<ID=ANN,Number=.,Type=String,Description="Functional annotations: 'Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO'">
##INFO=<ID=BaseCounts,Number=4,Type=Integer,Description="Counts of each base">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=CLNACC,Number=.,Type=String,Description="Variant Accession and Versions">
##INFO=<ID=CLNDBN,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=CLNDSDB,Number=.,Type=String,Description="Variant disease database name">
##INFO=<ID=CLNDSDBID,Number=.,Type=String,Description="Variant disease database ID">
##INFO=<ID=CLNORIGIN,Number=.,Type=String,Description="Allele Origin. One or more of the following values may be added: 0 - unknown; 1 - germline; 2 - somatic; 4 - inherited; 8 - paternal; 16 - maternal; 32 - de-novo; 64 - biparental; 128 - uniparental; 256 - not-tested; 512 - tested-inconclusive; 1073741824 - other">
##INFO=<ID=CLNSIG,Number=.,Type=String,Description="Variant Clinical Significance, 0 - Uncertain significance, 1 - not provided, 2 - Benign, 3 - Likely benign, 4 - Likely pathogenic, 5 - Pathogenic, 6 - drug response, 7 - histocompatibility, 255 - other">
##INFO=<ID=Cosmic..CNT,Number=1,Type=Integer,Description="How many samples have this mutation">
##INFO=<ID=Cosmic..CosmicID,Number=1,Type=String,Description="Cosmic ID. Added">
##INFO=<ID=Cosmic..SNP,Number=