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.