1#version 2.4 2## 3## fileformat=VCFv4.2 4## fileDate=Fri Sept 7 16:16:20 UTC 2018 5## reference=/cromwell_root/broad-references/hg19/v0/Homo_sapiens_assembly19.fasta 6## contig=<ID=1,length=249250621,assembly=b37> 7## contig=<ID=2,length=243199373,assembly=b37> 8## contig=<ID=3,length=198022430,assembly=b37> 9## contig=<ID=4,length=191154276,assembly=b37> 10## contig=<ID=5,length=180915260,assembly=b37> 11## contig=<ID=6,length=171115067,assembly=b37> 12## contig=<ID=7,length=159138663,assembly=b37> 13## contig=<ID=8,length=146364022,assembly=b37> 14## contig=<ID=9,length=141213431,assembly=b37> 15## contig=<ID=10,length=135534747,assembly=b37> 16## contig=<ID=11,length=135006516,assembly=b37> 17## contig=<ID=12,length=133851895,assembly=b37> 18## contig=<ID=13,length=115169878,assembly=b37> 19## contig=<ID=14,length=107349540,assembly=b37> 20## contig=<ID=15,length=102531392,assembly=b37> 21## contig=<ID=16,length=90354753,assembly=b37> 22## contig=<ID=17,length=81195210,assembly=b37> 23## contig=<ID=18,length=78077248,assembly=b37> 24## contig=<ID=19,length=59128983,assembly=b37> 25## contig=<ID=20,length=63025520,assembly=b37> 26## contig=<ID=21,length=48129895,assembly=b37> 27## contig=<ID=22,length=51304566,assembly=b37> 28## contig=<ID=X,length=155270560,assembly=b37> 29## contig=<ID=Y,length=59373566,assembly=b37> 30## contig=<ID=MT,length=16569,assembly=b37> 31## contig=<ID=GL000207.1,length=4262,assembly=b37> 32## contig=<ID=GL000226.1,length=15008,assembly=b37> 33## contig=<ID=GL000229.1,length=19913,assembly=b37> 34## contig=<ID=GL000231.1,length=27386,assembly=b37> 35## contig=<ID=GL000210.1,length=27682,assembly=b37> 36## contig=<ID=GL000239.1,length=33824,assembly=b37> 37## contig=<ID=GL000235.1,length=34474,assembly=b37> 38## contig=<ID=GL000201.1,length=36148,assembly=b37> 39## contig=<ID=GL000247.1,length=36422,assembly=b37> 40## contig=<ID=GL000245.1,length=36651,assembly=b37> 41## contig=<ID=GL000197.1,length=37175,assembly=b37> 42## contig=<ID=GL000203.1,length=37498,assembly=b37> 43## contig=<ID=GL000246.1,length=38154,assembly=b37> 44## contig=<ID=GL000249.1,length=38502,assembly=b37> 45## contig=<ID=GL000196.1,length=38914,assembly=b37> 46## contig=<ID=GL000248.1,length=39786,assembly=b37> 47## contig=<ID=GL000244.1,length=39929,assembly=b37> 48## contig=<ID=GL000238.1,length=39939,assembly=b37> 49## contig=<ID=GL000202.1,length=40103,assembly=b37> 50## contig=<ID=GL000234.1,length=40531,assembly=b37> 51## contig=<ID=GL000232.1,length=40652,assembly=b37> 52## contig=<ID=GL000206.1,length=41001,assembly=b37> 53## contig=<ID=GL000240.1,length=41933,assembly=b37> 54## contig=<ID=GL000236.1,length=41934,assembly=b37> 55## contig=<ID=GL000241.1,length=42152,assembly=b37> 56## contig=<ID=GL000243.1,length=43341,assembly=b37> 57## contig=<ID=GL000242.1,length=43523,assembly=b37> 58## contig=<ID=GL000230.1,length=43691,assembly=b37> 59## contig=<ID=GL000237.1,length=45867,assembly=b37> 60## contig=<ID=GL000233.1,length=45941,assembly=b37> 61## contig=<ID=GL000204.1,length=81310,assembly=b37> 62## contig=<ID=GL000198.1,length=90085,assembly=b37> 63## contig=<ID=GL000208.1,length=92689,assembly=b37> 64## contig=<ID=GL000191.1,length=106433,assembly=b37> 65## contig=<ID=GL000227.1,length=128374,assembly=b37> 66## contig=<ID=GL000228.1,length=129120,assembly=b37> 67## contig=<ID=GL000214.1,length=137718,assembly=b37> 68## contig=<ID=GL000221.1,length=155397,assembly=b37> 69## contig=<ID=GL000209.1,length=159169,assembly=b37> 70## contig=<ID=GL000218.1,length=161147,assembly=b37> 71## contig=<ID=GL000220.1,length=161802,assembly=b37> 72## contig=<ID=GL000213.1,length=164239,assembly=b37> 73## contig=<ID=GL000211.1,length=166566,assembly=b37> 74## contig=<ID=GL000199.1,length=169874,assembly=b37> 75## contig=<ID=GL000217.1,length=172149,assembly=b37> 76## contig=<ID=GL000216.1,length=172294,assembly=b37> 77## contig=<ID=GL000215.1,length=172545,assembly=b37> 78## contig=<ID=GL000205.1,length=174588,assembly=b37> 79## contig=<ID=GL000219.1,length=179198,assembly=b37> 80## contig=<ID=GL000224.1,length=179693,assembly=b37> 81## contig=<ID=GL000223.1,length=180455,assembly=b37> 82## contig=<ID=GL000195.1,length=182896,assembly=b37> 83## contig=<ID=GL000212.1,length=186858,assembly=b37> 84## contig=<ID=GL000222.1,length=186861,assembly=b37> 85## contig=<ID=GL000200.1,length=187035,assembly=b37> 86## contig=<ID=GL000193.1,length=189789,assembly=b37> 87## contig=<ID=GL000194.1,length=191469,assembly=b37> 88## contig=<ID=GL000225.1,length=211173,assembly=b37> 89## contig=<ID=GL000192.1,length=547496,assembly=b37> 90## contig=<ID=NC_007605,length=171823,assembly=b37> 91## GATKCommandLine=<ID=Funcotator,CommandLine="Funcotator --output /var/folders/q3/hw5cxmn52wq347lg7rb_mzlw0000gq/T/hashSetOrderingIssue.vcf.funcotator16581150221919567512.maf --ref-version hg19 --data-sources-path /Users/louisb/Workspace/gatk_java11/src/test/resources/large/funcotator/funcotator_dataSources/ --output-file-format MAF --variant /Users/louisb/Workspace/gatk_java11/src/test/resources/org/broadinstitute/hellbender/tools/funcotator/validationTestData/hashSetOrderingIssue.vcf --reference /Users/louisb/Workspace/gatk_java11/src/test/resources/large/Homo_sapiens_assembly19.fasta.gz --verbosity INFO --remove-filtered-variants false --five-prime-flank-size 5000 --three-prime-flank-size 0 --force-b37-to-hg19-reference-contig-conversion false --transcript-selection-mode CANONICAL --lookahead-cache-bp 100000 --interval-set-rule UNION --interval-padding 0 --interval-exclusion-padding 0 --interval-merging-rule ALL --read-validation-stringency SILENT --seconds-between-progress-updates 10.0 --disable-sequence-dictionary-validation false --create-output-bam-index true --create-output-bam-md5 false --create-output-variant-index true --create-output-variant-md5 false --lenient false --add-output-sam-program-record true --add-output-vcf-command-line true --cloud-prefetch-buffer 40 --cloud-index-prefetch-buffer -1 --disable-bam-index-caching false --sites-only-vcf-output false --help false --version false --showHidden false --QUIET false --use-jdk-deflater false --use-jdk-inflater false --gcs-max-retries 20 --gcs-project-for-requester-pays --disable-tool-default-read-filters false",Version="Unavailable",Date="September 24, 2019 at 9:58:20 AM EDT"> 92## source=Funcotator 93## Funcotator Unavailable | Date 20195824T095820 | Gencode 19 CANONICAL | Achilles 110303 | CGC full_2012_03-15 | ClinVar 12.03.20 | Cosmic 83 | CosmicFusion v83 | CosmicTissue v83 | DNARepairGenes 20171217T214737 | Familial_Cancer_Genes 20110905 | Gencode_XHGNC 75_37 | Gencode_XRefSeq 75_37 | HGNC Nov302017 | Simple_Uniprot 2014_12 | dbSNP 9606_b150 94Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Verification_Status Validation_Status Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score BAM_File Sequencer Tumor_Sample_UUID Matched_Norm_Sample_UUID Genome_Change Annotation_Transcript Transcript_Strand Transcript_Exon Transcript_Position cDNA_Change Codon_Change Protein_Change Other_Transcripts Refseq_mRNA_Id Refseq_prot_Id SwissProt_acc_Id SwissProt_entry_Id Description UniProt_AApos UniProt_Region UniProt_Site UniProt_Natural_Variations UniProt_Experimental_Info GO_Biological_Process GO_Cellular_Component GO_Molecular_Function COSMIC_overlapping_mutations COSMIC_fusion_genes COSMIC_tissue_types_affected COSMIC_total_alterations_in_gene Tumorscape_Amplification_Peaks Tumorscape_Deletion_Peaks TCGAscape_Amplification_Peaks TCGAscape_Deletion_Peaks DrugBank ref_context gc_content CCLE_ONCOMAP_overlapping_mutations CCLE_ONCOMAP_total_mutations_in_gene CGC_Mutation_Type CGC_Translocation_Partner CGC_Tumor_Types_Somatic CGC_Tumor_Types_Germline CGC_Other_Diseases DNARepairGenes_Activity_linked_to_OMIM FamilialCancerDatabase_Syndromes MUTSIG_Published_Results OREGANNO_ID OREGANNO_Values tumor_f t_alt_count t_ref_count n_alt_count n_ref_count Gencode_19_secondaryVariantClassification Achilles_Top_Genes CGC_Name CGC_GeneID CGC_Chr CGC_Chr_Band CGC_Cancer_Somatic_Mut CGC_Cancer_Germline_Mut CGC_Cancer_Syndrome CGC_Tissue_Type CGC_Cancer_Molecular_Genetics CGC_Other_Germline_Mut ClinVar_HGMD_ID ClinVar_SYM ClinVar_TYPE ClinVar_ASSEMBLY ClinVar_rs CosmicFusion_fusion_id DNARepairGenes_Chromosome_location_linked_to_NCBI_MapView DNARepairGenes_Accession_number_linked_to_NCBI_Entrez Familial_Cancer_Genes_Synonym Familial_Cancer_Genes_Reference Gencode_XHGNC_hgnc_id HGNC_HGNC_ID HGNC_Status HGNC_Locus_Type HGNC_Locus_Group HGNC_Previous_Symbols HGNC_Previous_Name HGNC_Synonyms HGNC_Name_Synonyms HGNC_Chromosome HGNC_Date_Modified HGNC_Date_Symbol_Changed HGNC_Date_Name_Changed HGNC_Accession_Numbers HGNC_Enzyme_IDs HGNC_Ensembl_Gene_ID HGNC_Pubmed_IDs HGNC_RefSeq_IDs HGNC_Gene_Family_ID HGNC_Gene_Family_Name HGNC_CCDS_IDs HGNC_Vega_ID HGNC_OMIM_ID(supplied_by_OMIM) HGNC_RefSeq(supplied_by_NCBI) HGNC_UniProt_ID(supplied_by_UniProt) HGNC_Ensembl_ID(supplied_by_Ensembl) HGNC_UCSC_ID(supplied_by_UCSC) Simple_Uniprot_alt_uniprot_accessions dbSNP_AC dbSNP_AF dbSNP_AN dbSNP_ASP dbSNP_ASS dbSNP_CAF dbSNP_CDA dbSNP_CFL dbSNP_COMMON dbSNP_DP dbSNP_DSS dbSNP_G5 dbSNP_G5A dbSNP_GENEINFO dbSNP_GNO dbSNP_HD dbSNP_INT dbSNP_KGPhase1 dbSNP_KGPhase3 dbSNP_LSD dbSNP_MTP dbSNP_MUT dbSNP_NOC dbSNP_NOV dbSNP_NSF dbSNP_NSM dbSNP_NSN dbSNP_OM dbSNP_OTH dbSNP_PM dbSNP_PMC dbSNP_R3 dbSNP_R5 dbSNP_REF dbSNP_RV dbSNP_S3D dbSNP_SAO dbSNP_SLO dbSNP_SSR dbSNP_SYN dbSNP_TOPMED dbSNP_TPA dbSNP_U3 dbSNP_U5 dbSNP_VC dbSNP_VP dbSNP_WGT dbSNP_WTD dbSNP_dbSNPBuildID dbSNP_ID dbSNP_FILTER HGNC_Entrez_Gene_ID(supplied_by_NCBI) dbSNP_RSPOS dbSNP_VLD 95SNRNP27 11017 __UNKNOWN__ hg19 2 70120910 70120910 + 5'UTR DEL A A - 3214822|397747233 byFrequency;by1000genomes __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ NA NA __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ g.chr2:70120910delA ENST00000244227.3 + 1 SNRNP27_ENST00000409116.1_5'Flank|SNRNP27_ENST00000488986.1_5'Flank NM_006857.2 NP_006848.1 Q8WVK2 SNR27_HUMAN small nuclear ribonucleoprotein U4/U6.U5 subunit 27 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ mRNA processing (GO:0006397)|RNA splicing (GO:0008380) nucleus (GO:0005634) nucleic acid binding (GO:0003676) biliary_tract(2)|breast(12)|central_nervous_system(44)|large_intestine(11)|pancreas(22) 91 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ GGGAAAAATGAAAGCTGTGTT 0.43640897755610975 __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ __UNKNOWN__ X76302 HGNC:30240 Approved gene with protein product protein-coding gene "small nuclear ribonucleoprotein 27kDa (U4/U6.U5)", "small nuclear ribonucleoprotein, U4/U6.U5 27kDa subunit" RY1, U4/U6.U5-27K "nucleic acid binding protein RY 1", "U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein" 2p13.3 2016-10-05 2016-03-11 X76302 ENSG00000124380 7931148, 9085842 NM_006857 CCDS33219 OTTHUMG00000152689 NM_006857 Q8WVK2 ENSG00000124380 uc002sfw.4 Q15410 | | | true|true false|false 0.6222,0.3778|0.6222,0.3778 false|false false|false 1|1 | false|false true|false true|false SNRNP27:11017|SNRNP27:11017 true|false false|false false|false true|false true|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false false|false true|true false|false false|false false|false 0|0 true|true 0|0 false|false 0.661217,0.338783| false|false false|false false|false DIV|DIV 0x05010002000517013e000200|0x050100020005000002000200 1|1 false|false 134|138 rs3214822|rs397747233 | 11017 70120910|70120912 true|false 96