Commit 37d89f1f authored by Pradat Yoann's avatar Pradat Yoann
Browse files

[dev] minor fixes

parent 5a5941bb
Hugo_Symbol Entrez_Gene_Id NCBI_Build Chromosome Start_Position End_Position Variant_Quality Filter Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 HGVSc HGVSp HGVSp_Short all_effects Location Gene Feature Feature_type cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation Consequence IMPACT STRAND SYMBOL_SOURCE HGNC_ID BIOTYPE CCDS ENSP SWISSPROT TREMBL UNIPARC EXON INTRON AF gnomAD_AF MAX_AF MAX_AF_POPS n_GT n_SS n_FA n_DP n_AD t_GT t_SS t_FA t_DP t_AD
FAM131C 348487 GRCh37 1 16386305 16386306 50 PASS Intron INS - - C rs542191066 - - c.451+58dup FAM131C,intron_variant,,ENST00000375662,NM_182623.2;CLCNKB,downstream_gene_variant,,ENST00000375667,NM_001165945.2;CLCNKB,downstream_gene_variant,,ENST00000375679,NM_000085.4;CLCNKB,downstream_gene_variant,,ENST00000431772,;FAM131C,intron_variant,,ENST00000494078,; 1:16386305-16386306 ENSG00000185519 ENST00000375662.4 Transcript - - - - - rs542191066 intron_variant MODIFIER -1 HGNC 26717 protein_coding CCDS41270.1 ENSP00000364814 Q96AQ9 UPI000022B016 5/6 0.3678 0.5051 SAS 0/0 2 0.0 11 11,0 0/1 2 0.33299999999999996 6 4,2
ZIC4 84107 GRCh37 3 147121630 147121631 50 PASS Intron DEL TC TC - rs142316820 TC TC c.135+120_135+121del ZIC4,intron_variant,,ENST00000383075,NM_032153.5;ZIC4,intron_variant,,ENST00000425731,NM_001168379.1;ZIC4,intron_variant,,ENST00000462748,;ZIC4,intron_variant,,ENST00000463250,;ZIC4,intron_variant,,ENST00000473123,;ZIC4,intron_variant,,ENST00000484399,;ZIC1,intron_variant,,ENST00000488404,;ZIC4,intron_variant,,ENST00000491672,NM_001243256.1;ZIC4,intron_variant,,ENST00000525172,NM_001168378.1;ZIC4,upstream_gene_variant,,ENST00000484586,;ZIC1,intron_variant,,ENST00000472523,;ZIC4,downstream_gene_variant,,ENST00000464144,; 3:147121630-147121631 ENSG00000174963 ENST00000525172.2 Transcript - - - - - rs142316820 intron_variant MODIFIER -1 HGNC 20393 protein_coding CCDS54652.1 ENSP00000435509 Q8N9L1 C9JZU7,C9JD04,C9J6T3,B3KPI4 UPI0001914D88 1/4 0/0 2 0.0 6 6,0 0/1 2 0.33299999999999996 6 4,2
EIF4G1 1981 GRCh37 3 184043926 184043927 50 PASS Intron DEL AC AC - rs34901174 AC AC c.3243+217_3243+218del EIF4G1,intron_variant,,ENST00000319274,;EIF4G1,intron_variant,,ENST00000342981,NM_182917.4;EIF4G1,intron_variant,,ENST00000346169,NM_198241.2;EIF4G1,intron_variant,,ENST00000350481,NM_198242.2;EIF4G1,intron_variant,,ENST00000352767,NM_001194947.1;EIF4G1,intron_variant,,ENST00000382330,NM_001194946.1;EIF4G1,intron_variant,,ENST00000392537,NM_198244.2;EIF4G1,intron_variant,,ENST00000411531,;EIF4G1,intron_variant,,ENST00000414031,;EIF4G1,intron_variant,,ENST00000424196,;EIF4G1,intron_variant,,ENST00000427845,;EIF4G1,intron_variant,,ENST00000434061,NM_004953.4;EIF4G1,intron_variant,,ENST00000435046,;EIF4G1,intron_variant,,ENST00000441154,;EIF2B5,intron_variant,,ENST00000444495,;EIF4G1,intron_variant,,ENST00000448284,;EIF4G1,downstream_gene_variant,,ENST00000421110,;EIF4G1,downstream_gene_variant,,ENST00000426123,;EIF4G1,downstream_gene_variant,,ENST00000427607,;EIF4G1,downstream_gene_variant,,ENST00000428387,;EIF4G1,downstream_gene_variant,,ENST00000444134,;EIF4G1,downstream_gene_variant,,ENST00000444861,;EIF4G1,downstream_gene_variant,,ENST00000450424,;EIF4G1,downstream_gene_variant,,ENST00000457456,;SNORD66,downstream_gene_variant,,ENST00000390856,NR_003055.1;EIF4G1,intron_variant,,ENST00000442406,;EIF4G1,intron_variant,,ENST00000466311,;EIF4G1,downstream_gene_variant,,ENST00000413967,;EIF4G1,upstream_gene_variant,,ENST00000422614,;EIF4G1,upstream_gene_variant,,ENST00000460829,;EIF4G1,upstream_gene_variant,,ENST00000464548,;EIF4G1,upstream_gene_variant,,ENST00000475721,;EIF4G1,upstream_gene_variant,,ENST00000482303,;EIF4G1,downstream_gene_variant,,ENST00000484862,;EIF4G1,downstream_gene_variant,,ENST00000493299,; 3:184043926-184043927 ENSG00000114867 ENST00000424196.1 Transcript - - - - - rs34901174 intron_variant MODIFIER 1 HGNC 3296 protein_coding CCDS54687.1 ENSP00000416255 Q04637 Q96I65,C9JWW9,C9JWH7,C9JSU8,C9J987,C9J6B6,C9J556 UPI00015E0966 20/31 0/0 2 0.0 7 7,0 0/1 2 0.667 6 2,4
STEAP1B 256227 GRCh37 7 22533452 22533453 50 PASS Frame_Shift_Del DEL CA CA - novel CA CA c.87_88del p.His29GlnfsTer24 p.H29Qfs*24 STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000404369,NM_001164460.1;STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000424363,;STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000439708,;STEAP1B,intron_variant,,ENST00000406890,NM_207342.2;STEAP1B,splice_region_variant,,ENST00000483679,; 7:22533452-22533453 ENSG00000105889 ENST00000404369.4 Transcript 503-504 87-88 29-30 HE/QX caTGag/caag - frameshift_variant,splice_region_variant HIGH -1 HGNC 41907 protein_coding CCDS56469.1 ENSP00000384370 C9JL51,C9JE84,B5MCI2 UPI000173A267 3/5 0/0 2 0.0 22 22,0 0/1 2 0.33299999999999996 6 4,2
TEX12 56158 GRCh37 11 112042480 112042480 50 PASS Intron DEL T T - rs1225064086 T T c.228-9del TEX12,intron_variant,,ENST00000280358,NM_031275.4;TEX12,intron_variant,,ENST00000530752,;AP002884.3,intron_variant,,ENST00000532612,;BCO2,upstream_gene_variant,,ENST00000357685,;BCO2,upstream_gene_variant,,ENST00000361053,NM_001256398.1;BCO2,upstream_gene_variant,,ENST00000393032,NM_031938.5;BCO2,upstream_gene_variant,,ENST00000438022,;BCO2,upstream_gene_variant,,ENST00000526088,NM_001037290.2,NM_001256397.1;BCO2,upstream_gene_variant,,ENST00000531169,;BCO2,upstream_gene_variant,,ENST00000532593,NM_001256400.1;RP11-356J5.4,intron_variant,,ENST00000527589,;SDHD,intron_variant,,ENST00000525468,;SDHD,intron_variant,,ENST00000525987,;SDHD,intron_variant,,ENST00000531744,;SDHD,intron_variant,,ENST00000532699,;BCO2,upstream_gene_variant,,ENST00000460924,;BCO2,upstream_gene_variant,,ENST00000461480,;BCO2,upstream_gene_variant,,ENST00000494860,;BCO2,upstream_gene_variant,,ENST00000527939,;BCO2,upstream_gene_variant,,ENST00000531003,;BCO2,upstream_gene_variant,,ENST00000534122,;BCO2,upstream_gene_variant,,ENST00000534550,; 11:112042480 ENSG00000150783 ENST00000280358.4 Transcript - - - - - rs1225064086 intron_variant MODIFIER 1 HGNC 11734 protein_coding CCDS31679.1 ENSP00000280358 Q9BXU0 UPI00001377E3 4/4 1.711e-05 8.319e-05 gnomAD_AFR 0/0 2 0.0 31 31,0 0/1 2 0.33299999999999996 6 4,2
KMT2D 8085 GRCh37 12 49431403 49431404 50 PASS Frame_Shift_Ins INS - - T novel - - c.9735dup p.Pro3246ThrfsTer5 p.P3246Tfs*5 KMT2D,frameshift_variant,p.Pro3246ThrfsTer5,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000549743,;KMT2D,downstream_gene_variant,,ENST00000549799,; 12:49431403-49431404 ENSG00000167548 ENST00000301067.7 Transcript 9735-9736 9735-9736 3245-3246 -/X -/A - frameshift_variant HIGH -1 HGNC 7133 protein_coding CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 34/54 0/0 2 0.0 48 48,0 0/1 2 0.212 33 26,7
PDS5B 23047 GRCh37 13 33332314 33332314 50 PASS Frame_Shift_Del DEL A A - novel A A c.3148del p.Thr1050GlnfsTer12 p.T1050Qfs*12 PDS5B,frameshift_variant,p.Thr1050GlnfsTer12,ENST00000315596,NM_015032.3;PDS5B,frameshift_variant,p.Thr4GlnfsTer12,ENST00000447833,;PDS5B,frameshift_variant,p.Thr1050GlnfsTer12,ENST00000450460,; 13:33332314 ENSG00000083642 ENST00000315596.10 Transcript 3332 3146 1049 Q/X cAa/ca - frameshift_variant HIGH 1 HGNC 20418 protein_coding CCDS41878.1 ENSP00000313851 Q9NTI5 UPI000006D4A9 27/35 0/0 2 0.0 47 47,0 0/1 2 0.33299999999999996 6 4,2
CCR7 1236 GRCh37 17 38712161 38712161 50 PASS Intron DEL T T - rs532551852 T T c.61-91del CCR7,intron_variant,,ENST00000246657,NM_001838.3;CCR7,intron_variant,,ENST00000578085,;CCR7,intron_variant,,ENST00000579344,; 17:38712161 ENSG00000126353 ENST00000246657.2 Transcript - - - - - rs532551852 intron_variant MODIFIER -1 HGNC 1608 protein_coding CCDS11369.1 ENSP00000246657 P32248 J3KTN5,J3KSS9,A0N0Q0 UPI0000001C2F 2/2 0.0008 0.004 EAS 0/0 2 0.0 5 5,0 0/1 2 0.33299999999999996 6 4,2
ATP9A 10079 GRCh37 20 50342307 50342308 50 PASS Intron DEL TC TC - novel TC TC c.327+50_327+51del ATP9A,intron_variant,,ENST00000311637,;ATP9A,intron_variant,,ENST00000338821,NM_006045.1;ATP9A,intron_variant,,ENST00000402822,;ATP9A,downstream_gene_variant,,ENST00000477492,;,regulatory_region_variant,,ENSR00001225305,; 20:50342307-50342308 ENSG00000054793 ENST00000338821.5 Transcript - - - - - - intron_variant MODIFIER -1 HGNC 13540 protein_coding CCDS33489.1 ENSP00000342481 O75110 Q2NLD0,B4DR18 UPI000004D334 3/27 0/0 2 0.0 22 22,0 0/1 2 0.4 15 9,6
Hugo_Symbol Entrez_Gene_Id NCBI_Build Chromosome Start_Position End_Position Variant_Quality Filter Variant_Classification Variant_Type Reference_Allele Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 HGVSc HGVSp HGVSp_Short all_effects Location Gene Feature Feature_type cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation Consequence IMPACT STRAND SYMBOL_SOURCE HGNC_ID BIOTYPE CCDS ENSP SWISSPROT TREMBL UNIPARC EXON INTRON AF gnomAD_AF MAX_AF MAX_AF_POPS n_GT n_SS n_FA n_DP n_AD t_GT t_SS t_FA t_DP t_AD Tumor_Sample Tumor_Sample_Barcode Matched_Norm_Sample_Barcode Tumor_Sample_Site
FAM131C 348487 GRCh37 1 16386305 16386306 50 PASS Intron INS - - C rs542191066 - - c.451+58dup FAM131C,intron_variant,,ENST00000375662,NM_182623.2;CLCNKB,downstream_gene_variant,,ENST00000375667,NM_001165945.2;CLCNKB,downstream_gene_variant,,ENST00000375679,NM_000085.4;CLCNKB,downstream_gene_variant,,ENST00000431772,;FAM131C,intron_variant,,ENST00000494078,; 1:16386305-16386306 ENSG00000185519 ENST00000375662.4 Transcript - - - - - rs542191066 intron_variant MODIFIER -1 HGNC 26717 protein_coding CCDS41270.1 ENSP00000364814 Q96AQ9 UPI000022B016 5/6 0.3678 0.5051 SAS 0/0 2 0.0 11 11,0 0/1 2 0.33299999999999996 6 4,2 TCGA-A1-A0SB TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 01
ZIC4 84107 GRCh37 3 147121630 147121631 50 PASS Intron DEL TC TC - rs142316820 TC TC c.135+120_135+121del ZIC4,intron_variant,,ENST00000383075,NM_032153.5;ZIC4,intron_variant,,ENST00000425731,NM_001168379.1;ZIC4,intron_variant,,ENST00000462748,;ZIC4,intron_variant,,ENST00000463250,;ZIC4,intron_variant,,ENST00000473123,;ZIC4,intron_variant,,ENST00000484399,;ZIC1,intron_variant,,ENST00000488404,;ZIC4,intron_variant,,ENST00000491672,NM_001243256.1;ZIC4,intron_variant,,ENST00000525172,NM_001168378.1;ZIC4,upstream_gene_variant,,ENST00000484586,;ZIC1,intron_variant,,ENST00000472523,;ZIC4,downstream_gene_variant,,ENST00000464144,; 3:147121630-147121631 ENSG00000174963 ENST00000525172.2 Transcript - - - - - rs142316820 intron_variant MODIFIER -1 HGNC 20393 protein_coding CCDS54652.1 ENSP00000435509 Q8N9L1 C9JZU7,C9JD04,C9J6T3,B3KPI4 UPI0001914D88 1/4 0/0 2 0.0 6 6,0 0/1 2 0.33299999999999996 6 4,2 TCGA-A1-A0SB TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 01
EIF4G1 1981 GRCh37 3 184043926 184043927 50 PASS Intron DEL AC AC - rs34901174 AC AC c.3243+217_3243+218del EIF4G1,intron_variant,,ENST00000319274,;EIF4G1,intron_variant,,ENST00000342981,NM_182917.4;EIF4G1,intron_variant,,ENST00000346169,NM_198241.2;EIF4G1,intron_variant,,ENST00000350481,NM_198242.2;EIF4G1,intron_variant,,ENST00000352767,NM_001194947.1;EIF4G1,intron_variant,,ENST00000382330,NM_001194946.1;EIF4G1,intron_variant,,ENST00000392537,NM_198244.2;EIF4G1,intron_variant,,ENST00000411531,;EIF4G1,intron_variant,,ENST00000414031,;EIF4G1,intron_variant,,ENST00000424196,;EIF4G1,intron_variant,,ENST00000427845,;EIF4G1,intron_variant,,ENST00000434061,NM_004953.4;EIF4G1,intron_variant,,ENST00000435046,;EIF4G1,intron_variant,,ENST00000441154,;EIF2B5,intron_variant,,ENST00000444495,;EIF4G1,intron_variant,,ENST00000448284,;EIF4G1,downstream_gene_variant,,ENST00000421110,;EIF4G1,downstream_gene_variant,,ENST00000426123,;EIF4G1,downstream_gene_variant,,ENST00000427607,;EIF4G1,downstream_gene_variant,,ENST00000428387,;EIF4G1,downstream_gene_variant,,ENST00000444134,;EIF4G1,downstream_gene_variant,,ENST00000444861,;EIF4G1,downstream_gene_variant,,ENST00000450424,;EIF4G1,downstream_gene_variant,,ENST00000457456,;SNORD66,downstream_gene_variant,,ENST00000390856,NR_003055.1;EIF4G1,intron_variant,,ENST00000442406,;EIF4G1,intron_variant,,ENST00000466311,;EIF4G1,downstream_gene_variant,,ENST00000413967,;EIF4G1,upstream_gene_variant,,ENST00000422614,;EIF4G1,upstream_gene_variant,,ENST00000460829,;EIF4G1,upstream_gene_variant,,ENST00000464548,;EIF4G1,upstream_gene_variant,,ENST00000475721,;EIF4G1,upstream_gene_variant,,ENST00000482303,;EIF4G1,downstream_gene_variant,,ENST00000484862,;EIF4G1,downstream_gene_variant,,ENST00000493299,; 3:184043926-184043927 ENSG00000114867 ENST00000424196.1 Transcript - - - - - rs34901174 intron_variant MODIFIER 1 HGNC 3296 protein_coding CCDS54687.1 ENSP00000416255 Q04637 Q96I65,C9JWW9,C9JWH7,C9JSU8,C9J987,C9J6B6,C9J556 UPI00015E0966 20/31 0/0 2 0.0 7 7,0 0/1 2 0.667 6 2,4 TCGA-A1-A0SB TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 01
STEAP1B 256227 GRCh37 7 22533452 22533453 50 PASS Frame_Shift_Del DEL CA CA - novel CA CA c.87_88del p.His29GlnfsTer24 p.H29Qfs*24 STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000404369,NM_001164460.1;STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000424363,;STEAP1B,frameshift_variant,p.His29GlnfsTer24,ENST00000439708,;STEAP1B,intron_variant,,ENST00000406890,NM_207342.2;STEAP1B,splice_region_variant,,ENST00000483679,; 7:22533452-22533453 ENSG00000105889 ENST00000404369.4 Transcript 503-504 87-88 29-30 HE/QX caTGag/caag - frameshift_variant,splice_region_variant HIGH -1 HGNC 41907 protein_coding CCDS56469.1 ENSP00000384370 C9JL51,C9JE84,B5MCI2 UPI000173A267 3/5 0/0 2 0.0 22 22,0 0/1 2 0.33299999999999996 6 4,2 TCGA-A1-A0SB TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 01
TEX12 56158 GRCh37 11 112042480 112042480 50 PASS Intron DEL T T - rs1225064086 T T c.228-9del TEX12,intron_variant,,ENST00000280358,NM_031275.4;TEX12,intron_variant,,ENST00000530752,;AP002884.3,intron_variant,,ENST00000532612,;BCO2,upstream_gene_variant,,ENST00000357685,;BCO2,upstream_gene_variant,,ENST00000361053,NM_001256398.1;BCO2,upstream_gene_variant,,ENST00000393032,NM_031938.5;BCO2,upstream_gene_variant,,ENST00000438022,;BCO2,upstream_gene_variant,,ENST00000526088,NM_001037290.2,NM_001256397.1;BCO2,upstream_gene_variant,,ENST00000531169,;BCO2,upstream_gene_variant,,ENST00000532593,NM_001256400.1;RP11-356J5.4,intron_variant,,ENST00000527589,;SDHD,intron_variant,,ENST00000525468,;SDHD,intron_variant,,ENST00000525987,;SDHD,intron_variant,,ENST00000531744,;SDHD,intron_variant,,ENST00000532699,;BCO2,upstream_gene_variant,,ENST00000460924,;BCO2,upstream_gene_variant,,ENST00000461480,;BCO2,upstream_gene_variant,,ENST00000494860,;BCO2,upstream_gene_variant,,ENST00000527939,;BCO2,upstream_gene_variant,,ENST00000531003,;BCO2,upstream_gene_variant,,ENST00000534122,;BCO2,upstream_gene_variant,,ENST00000534550,; 11:112042480 ENSG00000150783 ENST00000280358.4 Transcript - - - - - rs1225064086 intron_variant MODIFIER 1 HGNC 11734 protein_coding CCDS31679.1 ENSP00000280358 Q9BXU0 UPI00001377E3 4/4 1.711e-05 8.319e-05 gnomAD_AFR 0/0 2 0.0 31 31,0 0/1 2 0.33299999999999996 6 4,2 TCGA-A1-A0SB TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 01
KMT2D 8085 GRCh37 12 49431403 49431404 50 PASS Frame_Shift_Ins INS - - T novel - - c.9735dup p.Pro3246ThrfsTer5 p.P3246Tfs*5 KMT2D,frameshift_variant,p.Pro3246ThrfsTer5,ENST00000301067,NM_003482.3;KMT2D,upstream_gene_variant,,ENST00000549743,;KMT2D,downstream_gene_variant,,ENST00000549799,; 12:49431403-49431404 ENSG00000167548 ENST00000301067.7 Transcript 9735-9736 9735-9736 3245-3246 -/X -/A - frameshift_variant HIGH -1 HGNC 7133 protein_coding CCDS44873.1 ENSP00000301067 O14686 Q6PIA1,Q59FG6,F8VWW4 UPI0000EE84D6 34/54 0/0 2 0.0 48 48,0 0/1 2 0.212 33 26,7 TCGA-A1-A0SB TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 01
PDS5B 23047 GRCh37 13 33332314 33332314 50 PASS Frame_Shift_Del DEL A A - novel A A c.3148del p.Thr1050GlnfsTer12 p.T1050Qfs*12 PDS5B,frameshift_variant,p.Thr1050GlnfsTer12,ENST00000315596,NM_015032.3;PDS5B,frameshift_variant,p.Thr4GlnfsTer12,ENST00000447833,;PDS5B,frameshift_variant,p.Thr1050GlnfsTer12,ENST00000450460,; 13:33332314 ENSG00000083642 ENST00000315596.10 Transcript 3332 3146 1049 Q/X cAa/ca - frameshift_variant HIGH 1 HGNC 20418 protein_coding CCDS41878.1 ENSP00000313851 Q9NTI5 UPI000006D4A9 27/35 0/0 2 0.0 47 47,0 0/1 2 0.33299999999999996 6 4,2 TCGA-A1-A0SB TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 01
CCR7 1236 GRCh37 17 38712161 38712161 50 PASS Intron DEL T T - rs532551852 T T c.61-91del CCR7,intron_variant,,ENST00000246657,NM_001838.3;CCR7,intron_variant,,ENST00000578085,;CCR7,intron_variant,,ENST00000579344,; 17:38712161 ENSG00000126353 ENST00000246657.2 Transcript - - - - - rs532551852 intron_variant MODIFIER -1 HGNC 1608 protein_coding CCDS11369.1 ENSP00000246657 P32248 J3KTN5,J3KSS9,A0N0Q0 UPI0000001C2F 2/2 0.0008 0.004 EAS 0/0 2 0.0 5 5,0 0/1 2 0.33299999999999996 6 4,2 TCGA-A1-A0SB TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 01
ATP9A 10079 GRCh37 20 50342307 50342308 50 PASS Intron DEL TC TC - novel TC TC c.327+50_327+51del ATP9A,intron_variant,,ENST00000311637,;ATP9A,intron_variant,,ENST00000338821,NM_006045.1;ATP9A,intron_variant,,ENST00000402822,;ATP9A,downstream_gene_variant,,ENST00000477492,;,regulatory_region_variant,,ENSR00001225305,; 20:50342307-50342308 ENSG00000054793 ENST00000338821.5 Transcript - - - - - - intron_variant MODIFIER -1 HGNC 13540 protein_coding CCDS33489.1 ENSP00000342481 O75110 Q2NLD0,B4DR18 UPI000004D334 3/27 0/0 2 0.0 22 22,0 0/1 2 0.4 15 9,6 TCGA-A1-A0SB TCGA-A1-A0SB-01A-11D-A142-09 TCGA-A1-A0SB-10B-01D-A142-09 01
......@@ -12,7 +12,7 @@ Example of how to annotate a list of VCF from one project/study.
Example
-----------
python main/data/vcf/run/vcf2maf_tcga_GA.py \
python examples/run_example_tcga_GA.py \
--i_split 1 \
--n_split 1 \
--vcf2maf ~/Documents/biotools/informatics/VCF/mskcc-vcf2maf-5453f80/vcf2maf.pl \
......@@ -106,7 +106,7 @@ if __name__ == "__main__":
mask_vcf_file = df_meta["file_name_GA"] == vcf_file
index_vcf_file = mask_vcf_file[mask_vcf_file].index[0]
vcf_identifiers = {
dt_identifiers = {
"Tumor_Sample" : df_meta.loc[index_vcf_file, "tumor_sample"],
"Tumor_Sample_Barcode" : df_meta.loc[index_vcf_file, "tumor_sample_barcode"],
"Matched_Norm_Sample_Barcode" : df_meta.loc[index_vcf_file, "normal_sample_barcode"],
......@@ -115,27 +115,28 @@ if __name__ == "__main__":
#### get parameter values
col_normal = "NORMAL"
if vcf_identifiers["Tumor_Sample_Site"] == "01":
if dt_identifiers["Tumor_Sample_Site"] == "01":
col_tumor = "PRIMARY"
else:
col_tumor = "METASTATIC"
normal_id = vcf_identifiers["Matched_Norm_Sample_Barcode"],
tumor_id = vcf_identifiers["Tumor_Sample_Barcode"],
normal_id = dt_identifiers["Matched_Norm_Sample_Barcode"],
tumor_id = dt_identifiers["Tumor_Sample_Barcode"],
infos_n_reads = ["AD", "DP", "FA"]
infos_other = ["SS", "GT"]
run_annotator(
vcf_folder = vcf_folder,
vcf_file = vcf_file,
col_normal = col_normal,
col_tumor = col_tumor,
normal_id = normal_id,
tumor_id = tumor_id,
infos_n_reads = infos_n_reads,
infos_other = infos_other,
vcf2maf = args.vcf2maf,
vep_folder = args.vep_folder,
vep_data = args.vep_data,
fasta = args.fasta,
dt_folders = dt_folders
vcf_folder = vcf_folder,
vcf_file = vcf_file,
col_normal = col_normal,
col_tumor = col_tumor,
normal_id = normal_id,
tumor_id = tumor_id,
infos_n_reads = infos_n_reads,
infos_other = infos_other,
vcf2maf = args.vcf2maf,
vep_folder = args.vep_folder,
vep_data = args.vep_data,
fasta = args.fasta,
dt_folders = dt_folders,
dt_identifiers = dt_identifiers
)
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