##fileformat=VCFv4.1
##fileDate=@@IGNORE_ME@@
##source=bior_tjson_to_vcf
##CombineVariants="analysis_type=CombineVariants input_file=[] read_buffer_size=null phone_home=NO_ET gatk_key=/projects/bsi/bictools/apps/alignment/GenomeAnalysisTK/1.6-5-g557da77/Hossain.Asif_mayo.edu.key read_filter=[] intervals=null excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/data2/bsi/reference/sequence/human/ncbi/37.1/allchr.fa 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=-1 defaultBaseQualities=-1 validation_strictness=SILENT 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 logging_level=INFO log_to_file=null help=false variant=[(RodBinding name=variant source=/data2/bsi/RandD/sampleData/Genome_GPS/sb/exome/110815_SN316_0162_AD07MMACXX/variants//s_tumor/s_tumor.variants.chr22.raw.vcf), (RodBinding name=variant2 source=/data2/bsi/RandD/sampleData/Genome_GPS/sb/exome/110815_SN316_0162_AD07MMACXX/variants//s_tumor/s_tumor.variants.chr21.raw.vcf)] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub genotypemergeoption=PRIORITIZE filteredrecordsmergetype=KEEP_IF_ANY_UNFILTERED multipleallelesmergetype=BY_TYPE rod_priority_list=variant2,variant printComplexMerges=false filteredAreUncalled=false minimalVCF=false setKey=set assumeIdenticalSamples=false minimumN=1 suppressCommandLineHeader=false mergeInfoWithMaxAC=false filter_mismatching_base_and_quals=false"
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=1000Genomes.AFR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AFR based on AC/AN">
##INFO=<ID=1000Genomes.AMR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from AMR based on AC/AN">
##INFO=<ID=1000Genomes.ASN_AF,Number=1,Type=Float,Description="Allele Frequency for samples from ASN based on AC/AN">
##INFO=<ID=1000Genomes.EUR_AF,Number=1,Type=Float,Description="Allele Frequency for samples from EUR based on AC/AN">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=Approved_Gene_Name,Number=1,Type=String,Description="The official gene name that has been approved by the HGNC and is publicly available">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=BGI200_Danish_MAF,Number=1,Type=Float,Description="Estimated Minor Allele Frequency">
##INFO=<ID=COSMIC.Mutation_AA,Number=1,Type=String,Description="The change that has occurred in the peptide sequence as a result of the mutation">
##INFO=<ID=COSMIC.Mutation_CDS,Number=1,Type=String,Description="The change that has occurred in the nucleotide sequence as a result of the mutation">
##INFO=<ID=COSMIC.Mutation_ID,Number=1,Type=String,Description="This id is used to identify a mutation within the COSMIC database and is assigned as the mutation is curated">
##INFO=<ID=COSMIC.strand,Number=1,Type=String,Description="Strand based on GRCh37 genome build">
##INFO=<ID=dbSNP.build,Number=1,Type=Integer,Description="First dbSNP Build for RS">
##INFO=<ID=dbSNP.ClinicalSig,Number=.,Type=String,Description="Variant Clinical Significance, 0 - unknown, 1 - untested, 2 - non-pathogenic, 3 - probable-non-pathogenic, 4 - probable-pathogenic, 5 - pathogenic, 6 - drug-response, 7 - histocompatibility, 255 - other">
##INFO=<ID=dbSNP.DiseaseVariant,Number=.,Type=String,Description="Variant disease name">
##INFO=<ID=dbSNP.SNP_Allele_Origin,Number=1,Type=Integer,Description="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both">
##INFO=<ID=dbSNP.SuspectRegion,Number=1,Type=Integer,Description="Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other">
##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth; some reads may have been filtered">
##INFO=<ID=DS,Number=0,Type=Flag,Description="Were any of the samples downsampled?">
##INFO=<ID=Dels,Number=1,Type=Float,Description="Fraction of Reads Containing Spanning Deletions">
##INFO=<ID=ED,Number=1,Type=Integer,Description="Number of blat hits to reference genome, not counting self-hit">
##INFO=<ID=Ensembl_Gene_ID,Number=1,Type=String,Description="This column contains a manually curated Ensembl Gene ID">
##INFO=<ID=Entrez.GeneID,Number=1,Type=String,Description="Entrez Gene ID">
##INFO=<ID=ESP6500.AFR_MAF,Number=1,Type=Float,Description="African American Minor Allele Frequency (decimal value in the range 0.0 to 1.0)">
##INFO=<ID=ESP6500.EUR_MAF,Number=1,Type=Float,Description="European American Minor Allele Frequency (decimal value in the range 0.0 to 1.0)">
##INFO=<ID=FS,Number=1,Type=Float,Description="Phred-scaled p-value using Fisher's exact test to detect strand bias">
##INFO=<ID=Gene_Symbol,Number=1,Type=String,Description="Official Gene Symbol provided by HGNC">
##INFO=<ID=HRun,Number=1,Type=Integer,Description="Largest Contiguous Homopolymer Run of Variant Allele In Either Direction">
##INFO=<ID=HaplotypeScore,Number=1,Type=Float,Description="Consistency of the site with at most two segregating haplotypes">
##INFO=<ID=HapMap.CEU_MAF,Number=1,Type=Float,Description="Other allele frequency(Utah residents with Northern and Western European ancestry from the CEPH collection)">
##INFO=<ID=HapMap.CHB_MAF,Number=1,Type=Float,Description="Other Allele Frequency(Yoruban in Ibadan  Nigeria)">
##INFO=<ID=HapMap.JPT_MAF,Number=1,Type=Float,Description="Other Allele Frequency(Japanese in Tokyo Japan)">
##INFO=<ID=HapMap.YRI_MAF,Number=1,Type=Float,Description="Other Allele Frequency(Han Chinese in Beijing China)">
##INFO=<ID=InbreedingCoeff,Number=1,Type=Float,Description="Inbreeding coefficient as estimated from the genotype likelihoods per-sample when compared against the Hardy-Weinberg expectation">
##INFO=<ID=miRBASE.ID,Number=.,Type=String,Description="Semi-colon separated list of unique identifiers.  If this is a dbSNP variant  the rs number(s) should be used.  (VCF field)">
##INFO=<ID=MQ,Number=1,Type=Float,Description="RMS Mapping Quality">
##INFO=<ID=MQ0,Number=1,Type=Integer,Description="Total Mapping Quality Zero Reads">
##INFO=<ID=MQRankSum,Number=1,Type=Float,Description="Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities">
##INFO=<ID=OMIM.Disease,Number=1,Type=String,Description="Phenotypes observed">
##INFO=<ID=OMIM.ID,Number=1,Type=Integer,Description="Phenotype MIM Number">
##INFO=<ID=PolyPhen.Score,Number=.,Type=Float,Description="The PolyPhen score.">
##INFO=<ID=PolyPhen.TERM,Number=.,Type=String,Description="The PolyPhen prediction.">
##INFO=<ID=QD,Number=1,Type=Float,Description="Variant Confidence/Quality by Depth">
##INFO=<ID=ReadPosRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias">
##INFO=<ID=rsID,Number=.,Type=String,Description="Semi-colon separated list of unique identifiers.  If this is a dbSNP variant, the rs number(s) should be used.  (VCF field)">
##INFO=<ID=SB,Number=1,Type=Float,Description="Strand Bias">
##INFO=<ID=set,Number=1,Type=String,Description="Source VCF for the merged record in CombineVariants">
##INFO=<ID=SIFT.Score,Number=.,Type=Float,Description="The SIFT score.">
##INFO=<ID=SIFT.TERM,Number=.,Type=String,Description="The SIFT prediction.">
##INFO=<ID=SNPEFF.Amino_acid_change,Number=.,Type=String,Description="Amino acid change: old_AA AA_position/new_AA (e.g. 'E30K').">
##INFO=<ID=SNPEFF.Coding,Number=.,Type=String,Description="This field is 'CODING' if any transcript of the gene is marked as protein coding. {CODING, NON_CODING}">
##INFO=<ID=SNPEFF.Codon_change,Number=.,Type=String,Description="Codon change: old_codon/new_codon OR distance to transcript (in case of upstream / downstream).">
##INFO=<ID=SNPEFF.Effect,Number=.,Type=String,Description="Effect of this variant. {INTERGENIC, UPSTREAM, UTR_5_PRIME, UTR_5_DELETED, START_GAINED, SPLICE_SITE_ACCEPTOR, SPLICE_SITE_DONOR, START_LOST, SYNONYMOUS_START, CDS, GENE, TRANSCRIPT, EXON, EXON_DELETED, NON_SYNONYMOUS_CODING, SYNONYMOUS_CODING, FRAME_SHIFT, CODON_CHANGE, CODON_INSERTION, CODON_CHANGE_PLUS_CODON_INSERTION, CODON_DELETION, CODON_CHANGE_PLUS_CODON_DELETION, STOP_GAINED, SYNONYMOUS_STOP, STOP_LOST, INTRON, UTR_3_PRIME, UTR_3_DELETED, DOWNSTREAM, INTRON_CONSERVED, INTERGENIC_CONSERVED, INTRAGENIC, RARE_AMINO_ACID, NON_SYNONYMOUS_START}">
##INFO=<ID=SNPEFF.Effect_impact,Number=.,Type=String,Description="Effects are categorized by 'impact' categories to help users find more significant variants. {HIGH, MODERATE, LOW, MODIFIER}">
##INFO=<ID=SNPEFF.Exon,Number=.,Type=String,Description="Exon rank or Intron rank (e.g. '1' for the first exon, '2' for the second exon, etc.).">
##INFO=<ID=SNPEFF.Functional_class,Number=.,Type=String,Description="Functional class. {NONE, SILENT, MISSENSE, NONSENSE}">
##INFO=<ID=SNPEFF.Gene_bioType,Number=.,Type=String,Description="Transcript bioType, if available.">
##INFO=<ID=SNPEFF.Gene_name,Number=.,Type=String,Description="Gene name">
##INFO=<ID=SNPEFF.Transcript,Number=.,Type=String,Description="Transcript ID (usually ENSEMBL IDs).">
##INFO=<ID=UCSC.Alignability/Uniqueness,Number=1,Type=Integer,Description="Score from 0-1000(Indicates confidence of the annotation.Higher the score higher the confidence)">
##INFO=<ID=UCSC.BlacklistedRegion,Number=1,Type=Integer,Description="Score from 0-1000(Indicates confidence of the annotation.Higher the score higher the confidence)">
##INFO=<ID=UCSC.conservation,Number=1,Type=Integer,Description="Score from 0-1000 (conservation scores based on a phylo-HMM)">
##INFO=<ID=UCSC.enhancer,Number=1,Type=Integer,Description="Score from 0-1000(Elements that tested positive are assigned a score of 900 and where as negative are assigned score of 200)">
##INFO=<ID=UCSC.regulation,Number=1,Type=String,Description="unique ID to identify this regulatory region">
##INFO=<ID=UCSC.Repeat_Region,Number=1,Type=Integer,Description="Smith Waterman alignment score">
##INFO=<ID=UCSC.tfbs,Number=1,Type=Integer,Description="Score from 0-1000">
##INFO=<ID=UCSC.tss,Number=1,Type=Integer,Description="Score">
##INFO=<ID=UniprotID,Number=1,Type=String,Description="The UniProt identifier provided by the EBI.">
##INFO=<ID=VEP.Allele,Number=.,Type=String,Description="The variant allele used to calculate the consequence.">
##INFO=<ID=VEP.Amino_acids,Number=.,Type=String,Description="Only given if the variation affects the protein-coding sequence.">
##INFO=<ID=VEP.cDNA_position,Number=.,Type=String,Description="Relative position of base pair in cDNA sequence.">
##INFO=<ID=VEP.CDS_position,Number=.,Type=String,Description="Relative position of base pair in coding sequence.">
##INFO=<ID=VEP.Codons,Number=.,Type=String,Description="The alternative codons with the variant base in upper case.">
##INFO=<ID=VEP.Consequence,Number=.,Type=String,Description="Consequence type, a term defined by the Sequence Ontology (SO), of this variation.">
##INFO=<ID=VEP.Feature,Number=.,Type=String,Description="Ensembl stable ID of feature.">
##INFO=<ID=VEP.Feature_type,Number=.,Type=String,Description="Type of feature. Currently one of Transcript, RegulatoryFeature, MotifFeature.">
##INFO=<ID=VEP.Gene,Number=.,Type=String,Description="Ensembl stable ID of affected gene.">
##INFO=<ID=VEP.HGNC,Number=.,Type=String,Description="The HGNC gene identifier.">
##INFO=<ID=VEP.Protein_position,Number=.,Type=String,Description="Relative position of amino acid in protein.">
##UnifiedGenotyper="analysis_type=UnifiedGenotyper input_file=[/data2/bsi/RandD/sampleData/Genome_GPS//sb/exome/110815_SN316_0162_AD07MMACXX/variants/s_tumor/s_tumor.chr21-sorted.bam] read_buffer_size=null phone_home=NO_ET gatk_key=/projects/bsi/bictools/apps/alignment/GenomeAnalysisTK/1.6-5-g557da77/Hossain.Asif_mayo.edu.key read_filter=[] intervals=[chr21] excludeIntervals=null interval_set_rule=UNION interval_merging=ALL reference_sequence=/data2/bsi/reference/sequence/human/ncbi/37.1/allchr.fa nonDeterministicRandomSeed=false downsampling_type=BY_SAMPLE downsample_to_fraction=null downsample_to_coverage=250 baq=OFF baqGapOpenPenalty=40.0 performanceLog=null useOriginalQualities=false BQSR=null quantize_quals=-1 defaultBaseQualities=-1 validation_strictness=SILENT unsafe=null num_threads=4 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 logging_level=INFO log_to_file=null help=false genotype_likelihoods_model=BOTH p_nonref_model=EXACT heterozygosity=0.0010 pcr_error_rate=1.0E-4 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=30.0 standard_min_confidence_threshold_for_emitting=30.0 noSLOD=false annotateNDA=false alleles=(RodBinding name= source=UNBOUND) min_base_quality_score=17 max_deletion_fraction=0.05 max_alternate_alleles=2 min_indel_count_for_genotyping=5 min_indel_fraction_per_sample=0.25 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 noBandedIndel=false indelDebug=false ignoreSNPAlleles=false dbsnp=(RodBinding name= source=UNBOUND) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub NO_HEADER=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##contig=<ID=chr1,length=249250621>
##contig=<ID=chr10,length=135534747>
##contig=<ID=chr11,length=135006516>
##contig=<ID=chr12,length=133851895>
##contig=<ID=chr13,length=115169878>
##contig=<ID=chr14,length=107349540>
##contig=<ID=chr15,length=102531392>
##contig=<ID=chr16,length=90354753>
##contig=<ID=chr17,length=81195210>
##contig=<ID=chr18,length=78077248>
##contig=<ID=chr19,length=59128983>
##contig=<ID=chr2,length=243199373>
##contig=<ID=chr20,length=63025520>
##contig=<ID=chr21,length=48129895>
##contig=<ID=chr22,length=51304566>
##contig=<ID=chr3,length=198022430>
##contig=<ID=chr4,length=191154276>
##contig=<ID=chr5,length=180915260>
##contig=<ID=chr6,length=171115067>
##contig=<ID=chr7,length=159138663>
##contig=<ID=chr8,length=146364022>
##contig=<ID=chr9,length=141213431>
##contig=<ID=chrGL000191.1,length=106433>
##contig=<ID=chrGL000192.1,length=547496>
##contig=<ID=chrGL000193.1,length=189789>
##contig=<ID=chrGL000194.1,length=191469>
##contig=<ID=chrGL000195.1,length=182896>
##contig=<ID=chrGL000196.1,length=38914>
##contig=<ID=chrGL000197.1,length=37175>
##contig=<ID=chrGL000198.1,length=90085>
##contig=<ID=chrGL000199.1,length=169874>
##contig=<ID=chrGL000200.1,length=187035>
##contig=<ID=chrGL000201.1,length=36148>
##contig=<ID=chrGL000202.1,length=40103>
##contig=<ID=chrGL000203.1,length=37498>
##contig=<ID=chrGL000204.1,length=81310>
##contig=<ID=chrGL000205.1,length=174588>
##contig=<ID=chrGL000206.1,length=41001>
##contig=<ID=chrGL000207.1,length=4262>
##contig=<ID=chrGL000208.1,length=92689>
##contig=<ID=chrGL000209.1,length=159169>
##contig=<ID=chrGL000210.1,length=27682>
##contig=<ID=chrGL000211.1,length=166566>
##contig=<ID=chrGL000212.1,length=186858>
##contig=<ID=chrGL000213.1,length=164239>
##contig=<ID=chrGL000214.1,length=137718>
##contig=<ID=chrGL000215.1,length=172545>
##contig=<ID=chrGL000216.1,length=172294>
##contig=<ID=chrGL000217.1,length=172149>
##contig=<ID=chrGL000218.1,length=161147>
##contig=<ID=chrGL000219.1,length=179198>
##contig=<ID=chrGL000220.1,length=161802>
##contig=<ID=chrGL000221.1,length=155397>
##contig=<ID=chrGL000222.1,length=186861>
##contig=<ID=chrGL000223.1,length=180455>
##contig=<ID=chrGL000224.1,length=179693>
##contig=<ID=chrGL000225.1,length=211173>
##contig=<ID=chrGL000226.1,length=15008>
##contig=<ID=chrGL000227.1,length=128374>
##contig=<ID=chrGL000228.1,length=129120>
##contig=<ID=chrGL000229.1,length=19913>
##contig=<ID=chrGL000230.1,length=43691>
##contig=<ID=chrGL000231.1,length=27386>
##contig=<ID=chrGL000232.1,length=40652>
##contig=<ID=chrGL000233.1,length=45941>
##contig=<ID=chrGL000234.1,length=40531>
##contig=<ID=chrGL000235.1,length=34474>
##contig=<ID=chrGL000236.1,length=41934>
##contig=<ID=chrGL000237.1,length=45867>
##contig=<ID=chrGL000238.1,length=39939>
##contig=<ID=chrGL000239.1,length=33824>
##contig=<ID=chrGL000240.1,length=41933>
##contig=<ID=chrGL000241.1,length=42152>
##contig=<ID=chrGL000242.1,length=43523>
##contig=<ID=chrGL000243.1,length=43341>
##contig=<ID=chrGL000244.1,length=39929>
##contig=<ID=chrGL000245.1,length=36651>
##contig=<ID=chrGL000246.1,length=38154>
##contig=<ID=chrGL000247.1,length=36422>
##contig=<ID=chrGL000248.1,length=39786>
##contig=<ID=chrGL000249.1,length=38502>
##contig=<ID=chrM,length=16569>
##contig=<ID=chrX,length=155270560>
##contig=<ID=chrY,length=59373566>
##reference=file:///data2/bsi/reference/sequence/human/ncbi/37.1/allchr.fa
##BIOR=<ID="rsID",Operation="bior_annotate",DataType="String",Field="ID",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Semi-colon separated list of unique identifiers.  If this is a dbSNP variant, the rs number(s) should be used.  (VCF field)",ShortUniqueName="dbSNP137",Source="dbSNP",Version="137",Build="GRCh37.p5",Description="NCBI's dbSNP Variant Database",Path="/research/bsi/data/catalogs/bior/v1/dbSNP/137/00-All_GRCh37.tsv.bgz">
##BIOR=<ID="dbSNP.build",Operation="bior_annotate",DataType="Integer",Field="INFO.dbSNPBuildID",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="First dbSNP Build for RS",ShortUniqueName="dbSNP137",Source="dbSNP",Version="137",Build="GRCh37.p5",Description="NCBI's dbSNP Variant Database",Path="/research/bsi/data/catalogs/bior/v1/dbSNP/137/00-All_GRCh37.tsv.bgz">
##BIOR=<ID="dbSNP.SuspectRegion",Operation="bior_annotate",DataType="Integer",Field="INFO.SSR",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Variant Suspect Reason Codes (may be more than one value added together) 0 - unspecified, 1 - Paralog, 2 - byEST, 4 - oldAlign, 8 - Para_EST, 16 - 1kg_failed, 1024 - other",ShortUniqueName="dbSNP137",Source="dbSNP",Version="137",Build="GRCh37.p5",Description="NCBI's dbSNP Variant Database",Path="/research/bsi/data/catalogs/bior/v1/dbSNP/137/00-All_GRCh37.tsv.bgz">
##BIOR=<ID="dbSNP.SNP_Allele_Origin",Operation="bior_annotate",DataType="Integer",Field="INFO.SAO",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Variant Allele Origin: 0 - unspecified, 1 - Germline, 2 - Somatic, 3 - Both",ShortUniqueName="dbSNP137",Source="dbSNP",Version="137",Build="GRCh37.p5",Description="NCBI's dbSNP Variant Database",Path="/research/bsi/data/catalogs/bior/v1/dbSNP/137/00-All_GRCh37.tsv.bgz">
##BIOR=<ID="dbSNP.ClinicalSig",Operation="bior_annotate",DataType="String",Field="INFO.CLNSIG",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Variant Clinical Significance, 0 - unknown, 1 - untested, 2 - non-pathogenic, 3 - probable-non-pathogenic, 4 - probable-pathogenic, 5 - pathogenic, 6 - drug-response, 7 - histocompatibility, 255 - other",ShortUniqueName="dbSNP137_clinvar",Source="ClinVar",Version="137",Build="GRCh37.p5",Description="Variations from common_all.vcf.gz that are clinical",Path="/research/bsi/data/catalogs/bior/v1/dbSNP/137/clinvar_20130226_GRCh37.tsv.bgz">
##BIOR=<ID="dbSNP.DiseaseVariant",Operation="bior_annotate",DataType="String",Field="INFO.CLNDBN",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Variant disease name",ShortUniqueName="dbSNP137_clinvar",Source="ClinVar",Version="137",Build="GRCh37.p5",Description="Variations from common_all.vcf.gz that are clinical",Path="/research/bsi/data/catalogs/bior/v1/dbSNP/137/clinvar_20130226_GRCh37.tsv.bgz">
##BIOR=<ID="COSMIC.Mutation_ID",Operation="bior_annotate",DataType="String",Field="Mutation_ID",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="This id is used to identify a mutation within the COSMIC database and is assigned as the mutation is curated",ShortUniqueName="cosmic63",Source="Cosmic",Version="63",Build="GRCh37",Description="Catalogue Of Somatic Mutations In Cancer",Path="/research/bsi/data/catalogs/bior/v1/cosmic/v63/CosmicCompleteExport_GRCh37.tsv.bgz">
##BIOR=<ID="COSMIC.Mutation_CDS",Operation="bior_annotate",DataType="String",Field="Mutation_CDS",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="The change that has occurred in the nucleotide sequence as a result of the mutation",ShortUniqueName="cosmic63",Source="Cosmic",Version="63",Build="GRCh37",Description="Catalogue Of Somatic Mutations In Cancer",Path="/research/bsi/data/catalogs/bior/v1/cosmic/v63/CosmicCompleteExport_GRCh37.tsv.bgz">
##BIOR=<ID="COSMIC.Mutation_AA",Operation="bior_annotate",DataType="String",Field="Mutation_AA",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="The change that has occurred in the peptide sequence as a result of the mutation",ShortUniqueName="cosmic63",Source="Cosmic",Version="63",Build="GRCh37",Description="Catalogue Of Somatic Mutations In Cancer",Path="/research/bsi/data/catalogs/bior/v1/cosmic/v63/CosmicCompleteExport_GRCh37.tsv.bgz">
##BIOR=<ID="COSMIC.strand",Operation="bior_annotate",DataType="String",Field="Mutation_GRCh37_strand",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Strand based on GRCh37 genome build",ShortUniqueName="cosmic63",Source="Cosmic",Version="63",Build="GRCh37",Description="Catalogue Of Somatic Mutations In Cancer",Path="/research/bsi/data/catalogs/bior/v1/cosmic/v63/CosmicCompleteExport_GRCh37.tsv.bgz">
##BIOR=<ID="1000Genomes.ASN_AF",Operation="bior_annotate",DataType="Float",Field="INFO.ASN_AF",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Allele Frequency for samples from ASN based on AC/AN",ShortUniqueName="1kG_3",Source="1000_genomes",Version="3",Build="GRCh37",Description="1000 Genomes Project goal is to find most genetic variants that have frequencies of at least 1% in the populations studied.",Path="/research/bsi/data/catalogs/bior/v1/1000_genomes/20110521/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites_GRCh37.tsv.bgz">
##BIOR=<ID="1000Genomes.AMR_AF",Operation="bior_annotate",DataType="Float",Field="INFO.AMR_AF",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Allele Frequency for samples from AMR based on AC/AN",ShortUniqueName="1kG_3",Source="1000_genomes",Version="3",Build="GRCh37",Description="1000 Genomes Project goal is to find most genetic variants that have frequencies of at least 1% in the populations studied.",Path="/research/bsi/data/catalogs/bior/v1/1000_genomes/20110521/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites_GRCh37.tsv.bgz">
##BIOR=<ID="1000Genomes.AFR_AF",Operation="bior_annotate",DataType="Float",Field="INFO.AFR_AF",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Allele Frequency for samples from AFR based on AC/AN",ShortUniqueName="1kG_3",Source="1000_genomes",Version="3",Build="GRCh37",Description="1000 Genomes Project goal is to find most genetic variants that have frequencies of at least 1% in the populations studied.",Path="/research/bsi/data/catalogs/bior/v1/1000_genomes/20110521/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites_GRCh37.tsv.bgz">
##BIOR=<ID="1000Genomes.EUR_AF",Operation="bior_annotate",DataType="Float",Field="INFO.EUR_AF",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Allele Frequency for samples from EUR based on AC/AN",ShortUniqueName="1kG_3",Source="1000_genomes",Version="3",Build="GRCh37",Description="1000 Genomes Project goal is to find most genetic variants that have frequencies of at least 1% in the populations studied.",Path="/research/bsi/data/catalogs/bior/v1/1000_genomes/20110521/ALL.wgs.phase1_release_v3.20101123.snps_indels_sv.sites_GRCh37.tsv.bgz">
##BIOR=<ID="BGI200_Danish_MAF",Operation="bior_annotate",DataType="Float",Field="estimated_minor_allele_freq",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Estimated Minor Allele Frequency",ShortUniqueName="BGIhg19",Source="BGI",Version="hg19",Build="GRCh37 (lifted over from hg18)",Description="BGI and Danish Researchers Sequenced 200 Exomes  with targeted capture of 18 654 coding genes and sequence coverage of each individual exome at an average depth of 12-fold",Path="/research/bsi/data/catalogs/bior/v1/BGI/hg19/LuCAMP_200exomeFinal.maf_GRCh37.tsv.bgz">
##BIOR=<ID="ESP6500.EUR_MAF",Operation="bior_annotate",DataType="Float",Field="EA._maf",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="European American Minor Allele Frequency (decimal value in the range 0.0 to 1.0)",ShortUniqueName="ESP6500",Source="ESP",Version="6500",Build="GRCh37",Description="NHLBI GO Exome Sequencing Project (ESP) results to discover novel genes and mechanisms contributing to heart  lung and blood disorders",Path="/research/bsi/data/catalogs/bior/v1/ESP/build37/ESP6500SI_GRCh37.tsv.bgz">
##BIOR=<ID="ESP6500.AFR_MAF",Operation="bior_annotate",DataType="Float",Field="AA._maf",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="African American Minor Allele Frequency (decimal value in the range 0.0 to 1.0)",ShortUniqueName="ESP6500",Source="ESP",Version="6500",Build="GRCh37",Description="NHLBI GO Exome Sequencing Project (ESP) results to discover novel genes and mechanisms contributing to heart  lung and blood disorders",Path="/research/bsi/data/catalogs/bior/v1/ESP/build37/ESP6500SI_GRCh37.tsv.bgz">
##BIOR=<ID="HapMap.CEU_MAF",Operation="bior_annotate",DataType="Float",Field="CEU.otherallele_freq",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Other allele frequency(Utah residents with Northern and Western European ancestry from the CEPH collection)",ShortUniqueName="hapmap",Source="HapMap",Version="2010-08 phase2+3",Build="GRCh37 (lifted over from GRCh36)",Description="The International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings",Path="/research/bsi/data/catalogs/bior/v1/hapmap/2010-08_phaseII+III/allele_freqs_GRCh37.tsv.bgz">
##BIOR=<ID="HapMap.YRI_MAF",Operation="bior_annotate",DataType="Float",Field="CHB.otherallele_freq",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Other Allele Frequency(Han Chinese in Beijing China)",ShortUniqueName="hapmap",Source="HapMap",Version="2010-08 phase2+3",Build="GRCh37 (lifted over from GRCh36)",Description="The International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings",Path="/research/bsi/data/catalogs/bior/v1/hapmap/2010-08_phaseII+III/allele_freqs_GRCh37.tsv.bgz">
##BIOR=<ID="HapMap.JPT_MAF",Operation="bior_annotate",DataType="Float",Field="JPT.otherallele_freq",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Other Allele Frequency(Japanese in Tokyo Japan)",ShortUniqueName="hapmap",Source="HapMap",Version="2010-08 phase2+3",Build="GRCh37 (lifted over from GRCh36)",Description="The International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings",Path="/research/bsi/data/catalogs/bior/v1/hapmap/2010-08_phaseII+III/allele_freqs_GRCh37.tsv.bgz">
##BIOR=<ID="HapMap.CHB_MAF",Operation="bior_annotate",DataType="Float",Field="YRI.otherallele_freq",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Other Allele Frequency(Yoruban in Ibadan  Nigeria)",ShortUniqueName="hapmap",Source="HapMap",Version="2010-08 phase2+3",Build="GRCh37 (lifted over from GRCh36)",Description="The International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings",Path="/research/bsi/data/catalogs/bior/v1/hapmap/2010-08_phaseII+III/allele_freqs_GRCh37.tsv.bgz">
##BIOR=<ID="Entrez.GeneID",Operation="bior_annotate",DataType="String",Field="GeneID",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Entrez Gene ID",ShortUniqueName="gene37p10",Source="NCBI",Version="37p10",Build="GRCh37.p10",Description="NCBI's Gene Annotation directly from the gbs file",Path="/research/bsi/data/catalogs/bior/v1/NCBIGene/GRCh37_p10/genes.tsv.bgz">
##BIOR=<ID="Gene_Symbol",Operation="bior_annotate",DataType="String",Field="gene",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Official Gene Symbol provided by HGNC",ShortUniqueName="gene37p10",Source="NCBI",Version="37p10",Build="GRCh37.p10",Description="NCBI's Gene Annotation directly from the gbs file",Path="/research/bsi/data/catalogs/bior/v1/NCBIGene/GRCh37_p10/genes.tsv.bgz">
##BIOR=<ID="Approved_Gene_Name",Operation="bior_annotate",DataType="String",Field="Approved_Name",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="The official gene name that has been approved by the HGNC and is publicly available",ShortUniqueName="hgnc201208",Source="HGNC",Version="2012_08_12",Build="GRCh37",Description="Crossmaps from the HUGO Gene Nomenclature Committee that assigns standardised nomenclature to human genes.",Path="/research/bsi/data/catalogs/bior/v1/hgnc/2012_08_12/hgnc_GRCh37.tsv.bgz">
##BIOR=<ID="Ensembl_Gene_ID",Operation="bior_annotate",DataType="String",Field="Ensembl_Gene_ID",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="This column contains a manually curated Ensembl Gene ID",ShortUniqueName="hgnc201208",Source="HGNC",Version="2012_08_12",Build="GRCh37",Description="Crossmaps from the HUGO Gene Nomenclature Committee that assigns standardised nomenclature to human genes.",Path="/research/bsi/data/catalogs/bior/v1/hgnc/2012_08_12/hgnc_GRCh37.tsv.bgz">
##BIOR=<ID="UniprotID",Operation="bior_annotate",DataType="String",Field="UniProt_ID",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="The UniProt identifier provided by the EBI.",ShortUniqueName="hgnc201208",Source="HGNC",Version="2012_08_12",Build="GRCh37",Description="Crossmaps from the HUGO Gene Nomenclature Committee that assigns standardised nomenclature to human genes.",Path="/research/bsi/data/catalogs/bior/v1/hgnc/2012_08_12/hgnc_GRCh37.tsv.bgz">
##BIOR=<ID="OMIM.ID",Operation="bior_annotate",DataType="Integer",Field="MIM_Number",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Phenotype MIM Number",ShortUniqueName="OMIM",Source="OMIM",Version="2013_02_27",Build="GRCh37",Description="OMIM is a comprehensive authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily (Online Mendelian Inheritance in Man)",Path="/research/bsi/data/catalogs/bior/v1/omim/2013_02_27/genemap_GRCh37.tsv.bgz">
##BIOR=<ID="OMIM.Disease",Operation="bior_annotate",DataType="String",Field="Disorders",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Phenotypes observed",ShortUniqueName="OMIM",Source="OMIM",Version="2013_02_27",Build="GRCh37",Description="OMIM is a comprehensive authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily (Online Mendelian Inheritance in Man)",Path="/research/bsi/data/catalogs/bior/v1/omim/2013_02_27/genemap_GRCh37.tsv.bgz">
##BIOR=<ID="miRBASE.ID",Operation="bior_annotate",DataType="String",Field="ID",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Semi-colon separated list of unique identifiers.  If this is a dbSNP variant  the rs number(s) should be used.  (VCF field)",ShortUniqueName="miRBase19",Source="miRBase",Version="19",Build="GRCh37.p5",Description="The miRBase database is a searchable database of published miRNA sequences and annotation",Path="/research/bsi/data/catalogs/bior/v1/mirbase/release19/hsa_GRCh37.p5.tsv.bgz">
##BIOR=<ID="UCSC.BlacklistedRegion",Operation="bior_annotate",DataType="Integer",Field="score",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Score from 0-1000(Indicates confidence of the annotation.Higher the score higher the confidence)",ShortUniqueName="dacExcl19",Source="UCSC",Version="hg19",Build="GRCh37",Description="The DAC Blacklisted Regions aim to identify a comprehensive set of regions in the human genome that have anomalous  unstructured  high signal/read counts in next gen sequencing experiments independent of cell line and type of experiment.",Path="/research/bsi/data/catalogs/bior/v1/ucsc/hg19/wgEncodeDacMapabilityConsensusExcludable_GRCh37.tsv.bgz">
##BIOR=<ID="UCSC.conservation",Operation="bior_annotate",DataType="Integer",Field="score",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Score from 0-1000 (conservation scores based on a phylo-HMM)",ShortUniqueName="phastCons46Hg19",Source="UCSC",Version="hg19",Build="GRCh37",Description="UCSC - shows multiple alignments of 46 vertebrate species and measurements of evolutionary conservation using two methods (phastCons and phyloP) from the PHAST package for all species (vertebrate) and two subsets (primate and placental mammal).",Path="/research/bsi/data/catalogs/bior/v1/ucsc/hg19/phastConsElements46way_GRCh37.tsv.bgz">
##BIOR=<ID="UCSC.regulation",Operation="bior_annotate",DataType="String",Field="id",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="unique ID to identify this regulatory region",ShortUniqueName="oreganno19",Source="UCSC",Version="hg19",Build="GRCh37",Description="UCSC Open Regulatory Annotation (ORegAnno) - literature-curated regulatory regions transcription factor binding sites and regulatory polymorphisms",Path="/research/bsi/data/catalogs/bior/v1/ucsc/hg19/oreganno_GRCh37.tsv.bgz">
##BIOR=<ID="UCSC.tfbs",Operation="bior_annotate",DataType="Integer",Field="score",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Score from 0-1000",ShortUniqueName="tfbs19",Source="UCSC",Version="hg19",Build="GRCh37",Description="Describes the location and score of transcription factor binding sites conserved in the human/mouse/rat alignment. A binding site is considered to be conserved across the alignment if its score meets the threshold score for its binding matrix in all 3 species.",Path="/research/bsi/data/catalogs/bior/v1/ucsc/hg19/tfbsConsSites_GRCh37.tsv.bgz">
##BIOR=<ID="UCSC.tss",Operation="bior_annotate",DataType="Integer",Field="score",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Score",ShortUniqueName="tss19",Source="UCSC",Version="hg19",Build="GRCh37",Description="This track describes the location of transcription start sites (TSS) throughout the human genome along with a confidence measure for each TSS based on experimental evidence",Path="/research/bsi/data/catalogs/bior/v1/ucsc/hg19/switchDbTss_GRCh37.tsv.bgz">
##BIOR=<ID="UCSC.enhancer",Operation="bior_annotate",DataType="Integer",Field="score",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Score from 0-1000(Elements that tested positive are assigned a score of 900 and where as negative are assigned score of 200)",ShortUniqueName="vista19",Source="UCSC",Version="hg19",Build="GRCh37",Description="This source provides data that identifies distant-acting transcriptional enhancers in the human genome by coupling the identification of evolutionary conserved non-coding sequences with a moderate throughput mouse transgenesis enhancer assay",Path="/research/bsi/data/catalogs/bior/v1/ucsc/hg19/vistaEnhancers_GRCh37.tsv.bgz">
##BIOR=<ID="UCSC.Alignability/Uniqueness",Operation="bior_annotate",DataType="Integer",Field="score",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Score from 0-1000(Indicates confidence of the annotation.Higher the score higher the confidence)",ShortUniqueName="dukeExcl19",Source="UCSC",Version="hg19",Build="GRCh37",Description="The Duke Excluded Regions track displays genomic regions for which mapped sequence tags were filtered out before signal generation and peak calling for Open Chromatin: DNaseI HS and FAIRE tracks.",Path="/research/bsi/data/catalogs/bior/v1/ucsc/hg19/wgEncodeDukeMapabilityRegionsExcludable_GRCh37.tsv.bgz">
##BIOR=<ID="UCSC.Repeat_Region",Operation="bior_annotate",DataType="Integer",Field="swScore",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Smith Waterman alignment score",ShortUniqueName="rmsk19",Source="UCSC",Version="hg19",Build="GRCh37",Description="This track was created by using Arian Smit's RepeatMasker program  which screens DNA sequences for interspersed repeats and low complexity DNA sequences.",Path="/research/bsi/data/catalogs/bior/v1/ucsc/hg19/rmsk_GRCh37.tsv.bgz">
##BIOR=<ID="VEP.Allele",Operation="bior_annotate",DataType="String",Field="Allele",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="The variant allele used to calculate the consequence.",ShortUniqueName="vep",Source="vep",Version="2.7",Build="Ensembl Release 69",Description="Tool from Ensembl that predicts the functional consequences of known and unknown variants.",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/vep.datasource.properties">
##BIOR=<ID="VEP.Gene",Operation="bior_annotate",DataType="String",Field="Gene",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Ensembl stable ID of affected gene.",ShortUniqueName="vep",Source="vep",Version="2.7",Build="Ensembl Release 69",Description="Tool from Ensembl that predicts the functional consequences of known and unknown variants.",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/vep.datasource.properties">
##BIOR=<ID="VEP.Feature",Operation="bior_annotate",DataType="String",Field="Feature",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Ensembl stable ID of feature.",ShortUniqueName="vep",Source="vep",Version="2.7",Build="Ensembl Release 69",Description="Tool from Ensembl that predicts the functional consequences of known and unknown variants.",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/vep.datasource.properties">
##BIOR=<ID="VEP.Feature_type",Operation="bior_annotate",DataType="String",Field="Feature_type",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Type of feature. Currently one of Transcript, RegulatoryFeature, MotifFeature.",ShortUniqueName="vep",Source="vep",Version="2.7",Build="Ensembl Release 69",Description="Tool from Ensembl that predicts the functional consequences of known and unknown variants.",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/vep.datasource.properties">
##BIOR=<ID="VEP.Consequence",Operation="bior_annotate",DataType="String",Field="Consequence",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Consequence type, a term defined by the Sequence Ontology (SO), of this variation.",ShortUniqueName="vep",Source="vep",Version="2.7",Build="Ensembl Release 69",Description="Tool from Ensembl that predicts the functional consequences of known and unknown variants.",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/vep.datasource.properties">
##BIOR=<ID="VEP.cDNA_position",Operation="bior_annotate",DataType="String",Field="cDNA_position",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Relative position of base pair in cDNA sequence.",ShortUniqueName="vep",Source="vep",Version="2.7",Build="Ensembl Release 69",Description="Tool from Ensembl that predicts the functional consequences of known and unknown variants.",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/vep.datasource.properties">
##BIOR=<ID="VEP.CDS_position",Operation="bior_annotate",DataType="String",Field="CDS_position",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Relative position of base pair in coding sequence.",ShortUniqueName="vep",Source="vep",Version="2.7",Build="Ensembl Release 69",Description="Tool from Ensembl that predicts the functional consequences of known and unknown variants.",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/vep.datasource.properties">
##BIOR=<ID="VEP.Protein_position",Operation="bior_annotate",DataType="String",Field="Protein_position",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Relative position of amino acid in protein.",ShortUniqueName="vep",Source="vep",Version="2.7",Build="Ensembl Release 69",Description="Tool from Ensembl that predicts the functional consequences of known and unknown variants.",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/vep.datasource.properties">
##BIOR=<ID="VEP.Amino_acids",Operation="bior_annotate",DataType="String",Field="Amino_acids",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Only given if the variation affects the protein-coding sequence.",ShortUniqueName="vep",Source="vep",Version="2.7",Build="Ensembl Release 69",Description="Tool from Ensembl that predicts the functional consequences of known and unknown variants.",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/vep.datasource.properties">
##BIOR=<ID="VEP.Codons",Operation="bior_annotate",DataType="String",Field="Codons",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="The alternative codons with the variant base in upper case.",ShortUniqueName="vep",Source="vep",Version="2.7",Build="Ensembl Release 69",Description="Tool from Ensembl that predicts the functional consequences of known and unknown variants.",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/vep.datasource.properties">
##BIOR=<ID="VEP.HGNC",Operation="bior_annotate",DataType="String",Field="HGNC",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="The HGNC gene identifier.",ShortUniqueName="vep",Source="vep",Version="2.7",Build="Ensembl Release 69",Description="Tool from Ensembl that predicts the functional consequences of known and unknown variants.",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/vep.datasource.properties">
##BIOR=<ID="SIFT.TERM",Operation="bior_annotate",DataType="String",Field="SIFT_TERM",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="The SIFT prediction.",ShortUniqueName="vep",Source="vep",Version="2.7",Build="Ensembl Release 69",Description="Tool from Ensembl that predicts the functional consequences of known and unknown variants.",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/vep.datasource.properties">
##BIOR=<ID="SIFT.Score",Operation="bior_annotate",DataType="Float",Field="SIFT_Score",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="The SIFT score.",ShortUniqueName="vep",Source="vep",Version="2.7",Build="Ensembl Release 69",Description="Tool from Ensembl that predicts the functional consequences of known and unknown variants.",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/vep.datasource.properties">
##BIOR=<ID="PolyPhen.TERM",Operation="bior_annotate",DataType="String",Field="PolyPhen_TERM",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="The PolyPhen prediction.",ShortUniqueName="vep",Source="vep",Version="2.7",Build="Ensembl Release 69",Description="Tool from Ensembl that predicts the functional consequences of known and unknown variants.",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/vep.datasource.properties">
##BIOR=<ID="PolyPhen.Score",Operation="bior_annotate",DataType="Float",Field="PolyPhen_Score",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="The PolyPhen score.",ShortUniqueName="vep",Source="vep",Version="2.7",Build="Ensembl Release 69",Description="Tool from Ensembl that predicts the functional consequences of known and unknown variants.",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/vep.datasource.properties">
##BIOR=<ID="SNPEFF.Effect",Operation="bior_annotate",DataType="String",Field="Effect",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Effect of this variant. {INTERGENIC, UPSTREAM, UTR_5_PRIME, UTR_5_DELETED, START_GAINED, SPLICE_SITE_ACCEPTOR, SPLICE_SITE_DONOR, START_LOST, SYNONYMOUS_START, CDS, GENE, TRANSCRIPT, EXON, EXON_DELETED, NON_SYNONYMOUS_CODING, SYNONYMOUS_CODING, FRAME_SHIFT, CODON_CHANGE, CODON_INSERTION, CODON_CHANGE_PLUS_CODON_INSERTION, CODON_DELETION, CODON_CHANGE_PLUS_CODON_DELETION, STOP_GAINED, SYNONYMOUS_STOP, STOP_LOST, INTRON, UTR_3_PRIME, UTR_3_DELETED, DOWNSTREAM, INTRON_CONSERVED, INTERGENIC_CONSERVED, INTRAGENIC, RARE_AMINO_ACID, NON_SYNONYMOUS_START}",ShortUniqueName="snpeff",Source="snpeff",Version="2.0.5d",Build="GRCh37.64 (default)",Description="Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/snpeff.datasource.properties">
##BIOR=<ID="SNPEFF.Effect_impact",Operation="bior_annotate",DataType="String",Field="Effect_impact",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Effects are categorized by 'impact' categories to help users find more significant variants. {HIGH, MODERATE, LOW, MODIFIER}",ShortUniqueName="snpeff",Source="snpeff",Version="2.0.5d",Build="GRCh37.64 (default)",Description="Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/snpeff.datasource.properties">
##BIOR=<ID="SNPEFF.Functional_class",Operation="bior_annotate",DataType="String",Field="Functional_class",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Functional class. {NONE, SILENT, MISSENSE, NONSENSE}",ShortUniqueName="snpeff",Source="snpeff",Version="2.0.5d",Build="GRCh37.64 (default)",Description="Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/snpeff.datasource.properties">
##BIOR=<ID="SNPEFF.Codon_change",Operation="bior_annotate",DataType="String",Field="Codon_change",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Codon change: old_codon/new_codon OR distance to transcript (in case of upstream / downstream).",ShortUniqueName="snpeff",Source="snpeff",Version="2.0.5d",Build="GRCh37.64 (default)",Description="Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/snpeff.datasource.properties">
##BIOR=<ID="SNPEFF.Amino_acid_change",Operation="bior_annotate",DataType="String",Field="Amino_acid_change",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Amino acid change: old_AA AA_position/new_AA (e.g. 'E30K').",ShortUniqueName="snpeff",Source="snpeff",Version="2.0.5d",Build="GRCh37.64 (default)",Description="Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/snpeff.datasource.properties">
##BIOR=<ID="SNPEFF.Gene_name",Operation="bior_annotate",DataType="String",Field="Gene_name",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Gene name",ShortUniqueName="snpeff",Source="snpeff",Version="2.0.5d",Build="GRCh37.64 (default)",Description="Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/snpeff.datasource.properties">
##BIOR=<ID="SNPEFF.Gene_bioType",Operation="bior_annotate",DataType="String",Field="Gene_bioType",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Transcript bioType, if available.",ShortUniqueName="snpeff",Source="snpeff",Version="2.0.5d",Build="GRCh37.64 (default)",Description="Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/snpeff.datasource.properties">
##BIOR=<ID="SNPEFF.Coding",Operation="bior_annotate",DataType="String",Field="Coding",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="This field is 'CODING' if any transcript of the gene is marked as protein coding. {CODING, NON_CODING}",ShortUniqueName="snpeff",Source="snpeff",Version="2.0.5d",Build="GRCh37.64 (default)",Description="Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/snpeff.datasource.properties">
##BIOR=<ID="SNPEFF.Transcript",Operation="bior_annotate",DataType="String",Field="Transcript",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Transcript ID (usually ENSEMBL IDs).",ShortUniqueName="snpeff",Source="snpeff",Version="2.0.5d",Build="GRCh37.64 (default)",Description="Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/snpeff.datasource.properties">
##BIOR=<ID="SNPEFF.Exon",Operation="bior_annotate",DataType="String",Field="Exon",Number=".",Delimiter="|",EscapedDelimiter="\|",FieldDescription="Exon rank or Intron rank (e.g. '1' for the first exon, '2' for the second exon, etc.).",ShortUniqueName="snpeff",Source="snpeff",Version="2.0.5d",Build="GRCh37.64 (default)",Description="Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).",Path="/Users/duffp/Documents/IdeaProjects/bior_pipeline/target/bior_pipeline-3.0.0-SNAPSHOT/conf/tools/snpeff.datasource.properties">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	s_tumor
chr21	9411327	.	C	G	884.22	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=2.004;DP=47;Dels=0.00;ED=5;FS=9.784;HRun=1;HaplotypeScore=0.0000;MQ=138.53;MQ0=0;MQRankSum=1.162;QD=18.81;ReadPosRankSum=0.144;SB=-78.71;set=variant2;SNPEFF.Functional_class=NONE;rsID=rs75025155;dbSNP.build=131;dbSNP.SuspectRegion=0;dbSNP.SNP_Allele_Origin=0;UCSC.Repeat_Region=693;SNPEFF.Effect_impact=MODIFIER;SNPEFF.Effect=INTERGENIC;VEP.Allele=G;VEP.Consequence=intergenic_variant	GT:AD:DP:GQ:PL	0/1:17,30:47:99:914,0,432
chr21	9411410	.	C	T	1060.02	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=-0.055;DP=71;Dels=0.00;ED=5;FS=0.000;HRun=1;HaplotypeScore=0.9469;MQ=138.95;MQ0=3;MQRankSum=-0.055;QD=14.93;ReadPosRankSum=-2.611;SB=-311.23;set=variant2;SNPEFF.Functional_class=NONE;rsID=rs78200054;dbSNP.build=131;dbSNP.SuspectRegion=0;dbSNP.SNP_Allele_Origin=0;UCSC.Repeat_Region=693;SNPEFF.Effect_impact=MODIFIER;SNPEFF.Effect=INTERGENIC;VEP.Allele=T;VEP.Consequence=intergenic_variant	GT:AD:DP:GQ:PL	0/1:33,38:71:99:1090,0,817
chr21	9411500	.	G	T	1531.16	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=-6.149;DP=101;Dels=0.00;ED=5;FS=2.765;HRun=0;HaplotypeScore=0.0000;MQ=136.91;MQ0=2;MQRankSum=-0.467;QD=15.16;ReadPosRankSum=0.579;SB=-653.01;set=variant2;SNPEFF.Functional_class=NONE;rsID=rs71235073;dbSNP.build=130;dbSNP.SuspectRegion=0;dbSNP.SNP_Allele_Origin=0;UCSC.Repeat_Region=693;SNPEFF.Effect_impact=MODIFIER;SNPEFF.Effect=INTERGENIC;VEP.Allele=T;VEP.Consequence=intergenic_variant	GT:AD:DP:GQ:PL	0/1:46,55:101:99:1561,0,1280
chr21	9411602	.	T	C	977	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=-5.229;DP=112;Dels=0.00;ED=5;FS=0.000;HRun=0;HaplotypeScore=2.4131;MQ=107.17;MQ0=1;MQRankSum=2.874;QD=8.72;ReadPosRankSum=-0.506;SB=-328.91;set=variant2;SNPEFF.Functional_class=NONE;UCSC.Repeat_Region=693;SNPEFF.Effect_impact=MODIFIER;SNPEFF.Effect=INTERGENIC;VEP.Allele=C;VEP.Consequence=intergenic_variant	GT:AD:DP:GQ:PL	0/1:71,40:112:99:1007,0,1960
chr21	9411609	.	G	T	1095.35	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=1.076;DP=120;Dels=0.00;ED=5;FS=0.742;HRun=1;HaplotypeScore=4.3857;MQ=108.23;MQ0=1;MQRankSum=2.994;QD=9.13;ReadPosRankSum=-0.478;SB=-466.11;set=variant2;SNPEFF.Functional_class=NONE;rsID=rs76676778;dbSNP.build=131;dbSNP.SuspectRegion=0;dbSNP.SNP_Allele_Origin=0;UCSC.Repeat_Region=693;SNPEFF.Effect_impact=MODIFIER;SNPEFF.Effect=INTERGENIC;VEP.Allele=T;VEP.Consequence=intergenic_variant	GT:AD:DP:GQ:PL	0/1:79,41:120:99:1125,0,2184
chr21	9411635	.	C	T	243.31	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=4.264;DP=124;Dels=0.00;ED=5;FS=28.451;HRun=1;HaplotypeScore=19.6910;MQ=111.47;MQ0=1;MQRankSum=-5.653;QD=1.96;ReadPosRankSum=4.258;SB=-0.01;set=variant2;SNPEFF.Functional_class=NONE;UCSC.Repeat_Region=693;SNPEFF.Effect_impact=MODIFIER;SNPEFF.Effect=INTERGENIC;VEP.Allele=T;VEP.Consequence=intergenic_variant	GT:AD:DP:GQ:PL	0/1:99,25:124:99:273,0,3146
chr21	9411645	.	A	G	1103.37	PASS	AC=1;AF=0.50;AN=2;BaseQRankSum=-6.787;DP=121;Dels=0.00;ED=5;FS=3.568;HRun=0;HaplotypeScore=18.7077;MQ=116.17;MQ0=2;MQRankSum=1.748;QD=9.12;ReadPosRankSum=-2.226;SB=-452.55;set=variant2;SNPEFF.Functional_class=NONE;rsID=rs71235074;dbSNP.build=130;dbSNP.SuspectRegion=0;dbSNP.SNP_Allele_Origin=0;UCSC.Repeat_Region=693;SNPEFF.Effect_impact=MODIFIER;SNPEFF.Effect=INTERGENIC;VEP.Allele=G;VEP.Consequence=intergenic_variant	GT:AD:DP:GQ:PL	0/1:72,49:121:99:1133,0,1876
