Entering edit mode
22 months ago
Zahra
▴
110
Hi all
Here is the head .vcf file after annotation by ANNOVAR. (for tumor sample file)
Chr Start End Ref Alt Func.refGene Gene.refGene GeneDetail.refGene ExonicFunc.refGene AAChange.refGene Func_ensGene Gene_ensGene GeneDetail_ensGene ExonicFunc_ensGene AAChange_ensGene avsnp150 CLNALLELEID CLNDN CLNDISDB CLNREVSTAT CLNSIG Coding_CosmicV92 DamagePredCount SIFT_pred SIFT4G_pred Polyphen2_HDIV_pred Polyphen2_HVAR_pred LRT_pred MutationTaster_pred MutationAssessor_pred FATHMM_pred PROVEAN_pred VEST4_score MetaSVM_pred MetaLR_pred M.CAP_pred REVEL_score MutPred_score MVP_score MPC_score PrimateAI_pred DEOGEN2_pred BayesDel_addAF_pred BayesDel_noAF_pred ClinPred_pred LIST.S2_pred CADD_raw CADD_phred DANN_score fathmm.MKL_coding_pred fathmm.XF_coding_pred Eigen.raw_coding Eigen.phred_coding Eigen.PC.raw_coding Eigen.PC.phred_coding GenoCanyon_score integrated_fitCons_score GM12878_fitCons_score H1.hESC_fitCons_score HUVEC_fitCons_score LINSIGHT GERP.._NR GERP.._RS phyloP100way_vertebrate phyloP30way_mammalian phyloP17way_primate phastCons100way_vertebrate phastCons30way_mammalian phastCons17way_primate bStatistic Interpro_domain GTEx_V8_gene GTEx_V8_tissue AF AF_popmax AF_male AF_female AF_raw AF_afr AF_sas AF_amr AF_eas AF_nfe AF_fin AF_asj AF_oth non_topmed_AF_popmax non_neuro_AF_popmax non_cancer_AF_popmax controls_AF_popmax AF.1 AF_popmax.1 AF_male.1 AF_female.1 AF_raw.1 AF_afr.1 AF_sas.1 AF_amr.1 AF_eas.1 AF_nfe.1 AF_fin.1 AF_asj.1 AF_oth.1 non_topmed_AF_popmax.1 non_neuro_AF_popmax.1 non_cancer_AF_popmax.1 controls_AF_popmax.1 ICGC_Id ICGC_Occurrence Noncoding_CosmicV92 Mutation_type_DoCM_3.2 Info.CIViC InterVar_automated PVS1 PS1 PS2 PS3 PS4 PM1 PM2 PM3 PM4 PM5 PM6 PP1 PP2 PP3 PP4 PP5 BA1 BS1 BS2 BS3 BS4 BP1 BP2 BP3 BP4 BP5 BP6 BP7 Kaviar_AF Kaviar_AC Kaviar_AN Otherinfo1 Otherinfo2 Otherinfo3 Otherinfo4 Otherinfo5 Otherinfo6 Otherinfo7 Otherinfo8 Otherinfo9 Otherinfo10 Otherinfo11 Otherinfo12 Otherinfo13 Otherinfo14
chr12 53894576 53894576 - G upstream TARBP2 dist=129 . . ncRNA_exonic ENSG00000270175 . . . rs398019638 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.0858 0.0965 0.0867 0.0846 0.0860 0.0814 . 0.0532 0.0432 0.0965 0.0715 0.1469 0.0858 0.0948 0.0965 . 0.0922 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.00146 38 26028 0.25 . 19 chr12 53894576 rs398019638_53894576 C CG . GTQ;QUAL;badReads BRF=0.43;DB;FR=0.2500;HP=8;HapScore=2;MGOF=15;MMLQ=12;MQ=60.0;NF=5;NR=2;PP=139;QD=22.2857142857;SC=GAGGCGGGGTCGGGGGGGGCT;SOMATIC;SbPval=0.78;Source=Platypus;TC=28;TCF=15;TCR=13;TR=7;WE=53894584;WS=53894566 GT:GL:GOF:GQ:NR:NV 0/0:0.0,-4.0,-27.8:15:40:9:0 0/1:-16.58,0.0,-16.28:5:99:19:7
chr14 95555538 95555538 T - UTR3 DICER1 NM_001291628.1:c.*1297delA;NM_001271282.3:c.*1297delA;NM_177438.2:c.*1297delA;NM_001195573.1:c.*1413delA;NM_030621.4:c.*1297delA . . UTR3 ENSG00000100697 ENST00000526495:c.*1297delA;ENST00000343455:c.*1297delA;ENST00000393063:c.*1297delA . . rs899307216 . . . . . ID=COSV58616739;OCCURENCE=1(upper_aerodigestive_tract) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.0033 0.0098 0.0034 0.0032 0.0067 0.0049 . 0.0098 0.0046 0.0011 0.0083 0.0043 0.0072 0.0104 0.0055 . 0.0109 MU67398057 ORCA-IN|1|178|0.00561798 ID=COSV58616739;OCCURENCE=1(upper_aerodigestive_tract) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.0001537 4 26028 0.25 . 27 chr14 95555537 . GT G . VAFC BRF=0.27;FR=0.2501;HP=13;HapScore=3;MGOF=8;MMLQ=18;MQ=58.97;NF=7;NR=13;PP=214;QD=10.95;SC=GCCTAAAGAAGTTTTTTTTTT;SOMATIC;SbPval=0.52;Source=Platypus;TC=61;TCF=26;TCR=35;TR=20;WE=95555547;WS=95555527 GT:GL:GOF:GQ:NR:NV 0/0:0.0,-4.81,-47.2:4:48:34:2 1/0:-22.7,0.0,-3.1:8:31:27:18
chr14 95557516 95557516 C T intron DICER1 NM_001291628.1:exon25:c.5527+24G>A;NM_001271282.3:exon25:c.5527+24G>A;NM_177438.2:exon25:c.5527+24G>A;NM_030621.4:exon27:c.5527+24G>A . . intron ENSG00000100697 ENST00000526495:exon27:c.5527+24G>A;ENST00000343455:exon25:c.5527+24G>A;ENST00000393063:exon26:c.5527+24G>A;ENST00000527414:exon25:c.5527+24G>A;ENST00000556045:exon8:c.2221+24G>A . . rs759709100 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.196e-05 2.645e-05 1.473e-05 8.689e-06 1.193e-05 0 0 0 0 2.645e-05 0 0 0 2.694e-05 1.119e-05 2.929e-05 2.339e-05 . . . . . . . . . . . . . . . . . MU79342560 LIRI-JP|1|258|0.00387597 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1.94e-05 3 154602 0.25 . 35 chr14 95557516 . C T . PASS AF=0.00,0.37;MQ=60;SNP=.;SOMATIC GT:DP:DP4 0/0:36:22,14,0,0 0/1:35:10,12,8,5
chr14 95574595 95574595 T - intronic DICER1 . . . intronic ENSG00000100697 . . . rs878976709 . . . . . ID=COSV58626763;OCCURENCE=1(biliary_tract) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.0043 0.0063 0.0043 0.0043 0.0077 0.0044 . 0.0063 0 0.0035 0.0133 0.0123 0.0025 0.0067 0.0051 . 0.0052 MU111921835 BTCA-SG|2|71|0.028169 ID=COSV58626763;OCCURENCE=1(biliary_tract) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.0005379 14 26028 0.5 . 35 chr14 95574594 . GT G . VAFC BRF=0.27;FR=0.5000;HP=13;HapScore=4;MGOF=9;MMLQ=18;MQ=59.61;NF=16;NR=14;PP=417;QD=14.0666666667;SC=CTTACTACTAGTTTTTTTTTT;SOMATIC;SbPval=0.39;Source=Platypus;TC=58;TCF=28;TCR=30;TR=30;WE=95574604;WS=95574584 GT:GL:GOF:GQ:NR:NV 0/0:0.0,-5.23,-37.5:2:52:23:3 1/1:-43.2,-5.17,0.0:9:52:35:27
chr14 95593160 95593163 AAAA - intronic DICER1 . . . intronic ENSG00000100697 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.25 . 24 chr14 95593159 . CAAAA C . ALTC;QD;VAFC;badReads BRF=0.4;FR=0.2500;HP=14;HapScore=4;MGOF=15;MMLQ=12;MQ=57.48;NF=12;NR=19;PP=253;QD=8.29032258065;SC=TTTCAAAAAGCAAAAAAAAAA;SOMATIC;SbPval=0.77;Source=Platypus;TC=53;TCF=26;TCR=27;TR=31;WE=95593171;WS=95593147 GT:GL:GOF:GQ:NR:NV 0/0:0.0,-7.22,-73.1:11:72:29:13 0/1:-30.79,0.0,-18.39:15:99:24:18
chr16 24761873 24761873 A G intronic TNRC6A . . . intronic ENSG00000090905 . . . . . . . . . ID=COSV59371456;OCCURENCE=1(liver) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . MU3773188 LIRI-JP|1|258|0.00387597 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.25 . 40 chr16 24761873 . A G . PASS AF=0.00,0.50;MQ=60;SNP=.;SOMATIC GT:DP:DP4 0/0:33:20,13,0,0 0/1:40:12,8,9,11
chr16 24788148 24788148 T - intronic TNRC6A . . . intronic ENSG00000090905 . . . . . . . . . ID=COSV100170668;OCCURENCE=1(stomach) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . MU9052063 LIRI-JP|1|258|0.00387597,PACA-AU|1|391|0.00255754,GACA-JP|1|585|0.0017094 ID=COSV100170668;OCCURENCE=1(stomach) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.25 . 49 chr16 24788147 . GT G . PASS BRF=0.13;FR=0.2500;HP=8;HapScore=2;MGOF=8;MMLQ=31;MQ=60.0;NF=11;NR=9;PP=463;QD=24.2;SC=GAAAGCTTCTGTTTTTTTAGG;SOMATIC;SbPval=0.25;Source=Platypus;TC=83;TCF=35;TCR=48;TR=20;WE=24788156;WS=24788137 GT:GL:GOF:GQ:NR:NV 0/0:0.0,-8.73,-101.8:4:87:34:0 1/0:-49.35,0.0,-79.85:8:99:49:20
chr16 24802029 24802029 A - exonic TNRC6A . frameshift deletion TNRC6A:NM_001330520.3:exon6:c.2066delA:p.S690Vfs*19,TNRC6A:NM_001351850.2:exon6:c.2093delA:p.S699Vfs*19,TNRC6A:NM_014494.4:exon6:c.2066delA:p.S690Vfs*19 exonic ENSG00000090905 . frameshift deletion ENSG00000090905:ENST00000315183:exon6:c.2066delA:p.S690Vfs*19,ENSG00000090905:ENST00000395799:exon6:c.2066delA:p.S690Vfs*19 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . MU3773189 LIRI-JP|1|258|0.00387597 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.25 . 45 chr16 24802028 . GA G . PASS BRF=0.17;FR=0.2500;HP=3;HapScore=2;MGOF=8;MMLQ=25;MQ=59.58;NF=4;NR=14;PP=586;QD=34.4444444444;SC=AGGAACTGGGGAAAGTCAGAG;SOMATIC;SbPval=0.78;Source=Platypus;TC=69;TCF=17;TCR=52;TR=18;WE=24802037;WS=24802018 GT:GL:GOF:GQ:NR:NV 0/0:0.0,-6.92,-103.8:3:69:24:0 0/1:-62.96,0.0,-109.46:8:99:45:18
chr16 24807066 24807066 T G intronic TNRC6A . . . intronic ENSG00000090905 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0 . 45 chr16 24807066 . T G . FRQ;RE;SBAF;TAC AF=0.00,0.04;MQ=60;SNP=.;SOMATIC GT:DP:DP4 0/0:36:20,16,0,0 0/0:45:26,17,0,2
chr16 24833635 24833635 G T intronic TNRC6A . . . intronic ENSG00000090905 . . . . . . . . . ID=COSV59371481;OCCURENCE=1(liver) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . MU3773192 LIRI-JP|1|258|0.00387597 ID=COSV59371481;OCCURENCE=1(liver) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.25 . 38 chr16 24833635 . G T . PASS AF=0.00,0.55;MQ=60;SNP=.;SOMATIC GT:DP:DP4 0/0:21:10,11,0,0 0/1:38:7,10,12,9
chr16 24835952 24835952 A - UTR3 TNRC6A NM_001351850.2:c.*824delA;NM_001330520.3:c.*824delA;NM_014494.4:c.*824delA . . UTR3 ENSG00000090905 ENST00000315183:c.*824delA;ENST00000395799:c.*824delA;ENST00000491718:c.*6238delA;ENST00000450465:c.*824delA;ENST00000432286:c.*242delA . . rs35671423 . . . . . ID=COSV59362162;OCCURENCE=2(central_nervous_system) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.2798 0.3408 0.2769 0.2833 0.2550 0.1971 . 0.1744 0.0007 0.3408 0.3922 0.2370 0.2902 0.3435 0.3406 . 0.3678 MU75989519 COCA-CN|1|321|0.00311526 ID=COSV59362162;OCCURENCE=2(central_nervous_system) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.0363455 946 26028 0.25 . 42 chr16 24835951 rs35671423_24835951 CA C . VAFC BRF=0.32;DB;FR=0.2500;HP=11;HapScore=2;MGOF=15;MMLQ=25;MQ=59.49;NF=5;NR=9;PP=174;QD=13.2857142857;SC=ATGTAAAAGACAAAAAAAAAA;SOMATIC;SbPval=0.26;Source=Platypus;TC=62;TCF=36;TCR=26;TR=14;WE=24835960;WS=24835941 GT:GL:GOF:GQ:NR:NV 0/0:0.0,-6.32,-48.2:3:63:20:1 0/1:-19.59,0.0,-41.09:15:99:42:13
chr17 62495643 62495643 A - UTR3 DDX5 NM_001320597.2:c.*398delT;NM_001320596.2:c.*398delT;NM_001320595.2:c.*398delT;NM_004396.5:c.*398delT . . downstream ENSG00000108654 dist=91 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4.851e-05 0.0007 0 0.0001 0.0003 0 . 0 0.0007 0 0 0 0 0.0007 0.0007 . . MU111999412 COCA-CN|1|321|0.00311526,BTCA-SG|1|71|0.0140845 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 0.0001537 4 26028 0.25 . 46 chr17 62495642 . GA G . VAFC BRF=0.39;FR=0.2500;HP=10;HapScore=3;MGOF=13;MMLQ=26;MQ=58.56;NF=14;NR=12;PP=268;QD=10.7692307692;SC=TGTTTTCATGGAAAAAAAAAA;SOMATIC;SbPval=0.51;Source=Platypus;TC=86;TCF=44;TCR=42;TR=26;WE=62495651;WS=62495632 GT:GL:GOF:GQ:NR:NV 0/0:0.0,-11.64,-86.2:3:99:40:4 0/1:-28.95,0.0,-36.15:13:99:46:22
Now I don't know which of the variants are correct and acceptable. I would appreciate it if you could give me some hints.
