diff --git a/annotationPipeline/src/test/resources/expected/corner_cases.mskcc.txt b/annotationPipeline/src/test/resources/expected/corner_cases.mskcc.txt index 5964fd3c..70891097 100644 --- a/annotationPipeline/src/test/resources/expected/corner_cases.mskcc.txt +++ b/annotationPipeline/src/test/resources/expected/corner_cases.mskcc.txt @@ -1,4 +1,4 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT +#genome_nexus_version: 1.0.2 #isoform: mskcc Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence 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 t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/corner_cases.two_tumor_seq_allele.mskcc.txt b/annotationPipeline/src/test/resources/expected/corner_cases.two_tumor_seq_allele.mskcc.txt index bc4cbdd1..fe245c40 100644 --- a/annotationPipeline/src/test/resources/expected/corner_cases.two_tumor_seq_allele.mskcc.txt +++ b/annotationPipeline/src/test/resources/expected/corner_cases.two_tumor_seq_allele.mskcc.txt @@ -1,4 +1,4 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT +#genome_nexus_version: 1.0.2 #isoform: mskcc Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence 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 t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/corner_cases.two_tumor_seq_allele.uniprot.txt b/annotationPipeline/src/test/resources/expected/corner_cases.two_tumor_seq_allele.uniprot.txt index 1f018a0f..7b6ec286 100644 --- a/annotationPipeline/src/test/resources/expected/corner_cases.two_tumor_seq_allele.uniprot.txt +++ b/annotationPipeline/src/test/resources/expected/corner_cases.two_tumor_seq_allele.uniprot.txt @@ -1,4 +1,4 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT +#genome_nexus_version: 1.0.2 #isoform: uniprot Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence 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 t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status PCM1 5108 GRCh37 8 17796382 17796383 + frameshift_variant Frame_Shift_Ins INS - AAC A ENST00000325083.8:c.476dup p.Asn159LysfsTer14 p.N159Kfs*14 ENST00000325083 NM_006197.3 159 aac/aaAc 5/39 SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/corner_cases.uniprot.txt b/annotationPipeline/src/test/resources/expected/corner_cases.uniprot.txt index c34599e5..e7610db9 100644 --- a/annotationPipeline/src/test/resources/expected/corner_cases.uniprot.txt +++ b/annotationPipeline/src/test/resources/expected/corner_cases.uniprot.txt @@ -1,4 +1,4 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT +#genome_nexus_version: 1.0.2 #isoform: uniprot Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence 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 t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status MET 4233 GRCh37 7 116411872 116411900 + splice_region_variant,intron_variant Splice_Region DEL TAACAAGCTCTTTCTTTCTCTCTGTTTTA - - ENST00000397752.3:c.2888-31_2888-3del p.X963_splice ENST00000397752 NM_000245.2 963 SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.mskcc.txt b/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.mskcc.txt index c90ad22d..b4a00642 100644 --- a/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.mskcc.txt +++ b/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.mskcc.txt @@ -1,4 +1,4 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT +#genome_nexus_version: 1.0.2 #isoform: mskcc Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence 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 t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS @@ -12,20 +12,20 @@ NOTCH4 GRCh37 6 32188823 32188823 + missense_variant Missense_Mutation SNP G G MLL3 GRCh37 7 151945083 151945083 + missense_variant Missense_Mutation SNP C C T P-0000004-T01-IM3 84 11 ENST00000262189.6:c.2436G>A p.Met812Ile p.M812I ENST00000262189 NM_170606.2 812 atG/atA 14/59 SUCCESS MLL2 GRCh37 12 49433883 49433883 + missense_variant Missense_Mutation SNP G G A rs189888707 P-0000004-T01-IM3 247 16 ENST00000301067.7:c.7670C>T p.Pro2557Leu p.P2557L ENST00000301067 NM_003482.3 2557 cCg/cTg 31/54 SUCCESS TSHR GRCh37 14 81422178 81422178 + missense_variant Missense_Mutation SNP C C A rs2234919 P-0000004-T01-IM3 195 13 ENST00000298171.2:c.154C>A p.Pro52Thr p.P52T ENST00000298171 NM_000369.2 52 Ccc/Acc 1/10 SUCCESS -AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000349310.3:c.49G>A p.Glu17Lys p.E17K ENST00000349310 NM_001014432.1 17 Gag/Aag 4/15 SUCCESS +AKT1 GRCh37 14 105246551 105246551 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs121434592 P-0000004-T01-IM3 202 244 ENST00000407796.2:c.49G>A p.Glu17Lys p.E17K ENST00000407796 NM_001014431.1 17 Gag/Aag 3/14 SUCCESS TSC2 GRCh37 16 2110795 2110795 + missense_variant Missense_Mutation SNP G G A rs1800725 P-0000004-T01-IM3 236 22 ENST00000219476.3:c.1100G>A p.Arg367Gln p.R367Q ENST00000219476 NM_000548.3 367 cGg/cAg 11/42 SUCCESS -RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000407977.2:c.575C>T p.Pro192Leu p.P192L ENST00000407977 192 cCg/cTg 5/10 SUCCESS +RNF43 GRCh37 17 56440643 56440643 + missense_variant Missense_Mutation SNP G G A rs139557480 P-0000004-T01-IM3 296 41 ENST00000577716.1:c.575C>T p.Pro192Leu p.P192L ENST00000577716 NM_017763.4 192 cCg/cTg 5/10 SUCCESS NOTCH3 GRCh37 19 15303190 15303190 + missense_variant,splice_region_variant Missense_Mutation SNP C C T rs143385744 P-0000004-T01-IM3 274 17 ENST00000263388.2:c.338G>A p.Arg113Gln p.R113Q ENST00000263388 NM_000435.2 113 cGa/cAa 3/33 SUCCESS TP53 GRCh37 17 7578503 7578518 + frameshift_variant Frame_Shift_Del DEL CAGGGCAGGTCTTGGC CAGGGCAGGTCTTGGC - P-0000004-T01-IM3 209 58 ENST00000269305.4:c.412_427del p.Ala138CysfsTer27 p.A138Cfs*27 ENST00000269305 NM_001126112.2 138 GCCAAGACCTGCCCTGtg/tg 5/11 SUCCESS ALK GRCh37 2 29450535 29450535 + missense_variant Missense_Mutation SNP C C T P-0000015-T01-IM3 196 47 ENST00000389048.3:c.2819G>A p.Gly940Asp p.G940D ENST00000389048 NM_004304.4 940 gGc/gAc 17/29 SUCCESS PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000015-T01-IM3 80 56 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS -ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000206249.3:c.1607T>A p.Leu536His p.L536H ENST00000206249 NM_000125.3 536 cTc/cAc 8/8 SUCCESS +ESR1 GRCh37 6 152419920 152419920 + missense_variant Missense_Mutation SNP T T A P-0000015-T01-IM3 78 45 ENST00000443427.1:c.1607T>A p.Leu536His p.L536H ENST00000443427 NM_001122740.1 536 cTc/cAc 9/9 SUCCESS CDK4 GRCh37 12 58144485 58144485 + missense_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 346 84 ENST00000257904.6:c.586G>C p.Asp196His p.D196H ENST00000257904 NM_000075.3 196 Gac/Cac 5/8 SUCCESS TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000015-T01-IM3 131 61 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS -RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000407977.2:c.581G>C p.Trp194Ser p.W194S ENST00000407977 194 tGg/tCg 5/10 SUCCESS -GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000346208.3:c.1003dup p.Asp335GlyfsTer17 p.D335Gfs*17 ENST00000346208 333 -/G 5/6 SUCCESS -LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000253339.5:c.2348A>T p.Asp783Val p.D783V ENST00000253339 783 gAc/gTc 4/7 SUCCESS -LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000253339.5:c.187C>T p.Arg63Ter p.R63* ENST00000253339 63 Cga/Tga 1/7 SUCCESS +RNF43 GRCh37 17 56440637 56440637 + missense_variant,splice_region_variant Missense_Mutation SNP C C G P-0000015-T01-IM3 775 79 ENST00000577716.1:c.581G>C p.Trp194Ser p.W194S ENST00000577716 NM_017763.4 194 tGg/tCg 5/10 SUCCESS +GATA3 GRCh37 10 8111513 8111514 + frameshift_variant Frame_Shift_Ins INS - - G P-0000015-T01-IM3 378 75 ENST00000379328.3:c.1006dup p.Asp336GlyfsTer17 p.D336Gfs*17 ENST00000379328 NM_001002295.1 334 -/G 5/6 SUCCESS +LATS1 GRCh37 6 150001256 150001256 + missense_variant Missense_Mutation SNP T T A P-0000023-T01-IM3 440 91 ENST00000543571.1:c.2348A>T p.Asp783Val p.D783V ENST00000543571 NM_004690.3 783 gAc/gTc 5/8 SUCCESS +LATS1 GRCh37 6 150023076 150023076 + stop_gained Nonsense_Mutation SNP G G A rs187759014 P-0000023-T01-IM3 511 38 ENST00000543571.1:c.187C>T p.Arg63Ter p.R63* ENST00000543571 NM_004690.3 63 Cga/Tga 2/8 SUCCESS U2AF1 GRCh37 21 44514647 44514647 + missense_variant Missense_Mutation SNP T T C P-0000023-T01-IM3 291 60 ENST00000291552.4:c.509A>G p.Asn170Ser p.N170S ENST00000291552 NM_006758.2 170 aAc/aGc 7/8 SUCCESS BAP1 GRCh37 3 52439259 52439259 + frameshift_variant Frame_Shift_Del DEL G G - P-0000023-T01-IM3 179 60 ENST00000460680.1:c.983del p.Pro328LeufsTer7 p.P328Lfs*7 ENST00000460680 NM_004656.3 328 cCt/ct 11/17 SUCCESS LATS2 GRCh37 13 21555731 21555732 + frameshift_variant Frame_Shift_Ins INS - - A P-0000023-T01-IM3 232 119 ENST00000382592.4:c.2538dup p.Asn847Ter p.N847* ENST00000382592 NM_014572.2 846 -/T 6/8 SUCCESS @@ -33,12 +33,12 @@ CTNNB1 GRCh37 3 41266113 41266113 + missense_variant Missense_Mutation SNP C C PTEN GRCh37 10 89692904 89692904 + missense_variant Missense_Mutation SNP C C G rs121909224 P-0000024-T01-IM3 846 231 ENST00000371953.3:c.388C>G p.Arg130Gly p.R130G ENST00000371953 NM_000314.4 130 Cga/Gga 5/9 SUCCESS BCOR GRCh37 X 39921444 39921444 + missense_variant Missense_Mutation SNP T T C rs199538037 P-0000024-T01-IM3 647 317 ENST00000378444.4:c.4376A>G p.Asn1459Ser p.N1459S ENST00000378444 NM_001123385.1 1459 aAt/aGt 10/15 SUCCESS ARID1A GRCh37 1 27105878 27105881 + frameshift_variant Frame_Shift_Del DEL AGCT AGCT - P-0000024-T01-IM3 527 234 ENST00000324856.7:c.5489_5492del p.Lys1830MetfsTer52 p.K1830Mfs*52 ENST00000324856 NM_006015.4 1830 aAGCTt/at 20/20 SUCCESS -PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000274335.5:c.1746-8_1748del p.X582_splice ENST00000274335 582 13/15 SUCCESS +PIK3R1 GRCh37 5 67591238 67591248 + splice_acceptor_variant,coding_sequence_variant,intron_variant Splice_Site DEL TGTTTTTCAGG TGTTTTTCAGG - P-0000024-T01-IM3 762 445 ENST00000521381.1:c.1746-8_1748del p.X582_splice ENST00000521381 NM_181523.2 582 14/16 SUCCESS PTEN GRCh37 10 89720720 89720721 + frameshift_variant Frame_Shift_Ins INS - - A rs786204905 P-0000024-T01-IM3 170 53 ENST00000371953.3:c.875dup p.Asn292LysfsTer6 p.N292Kfs*6 ENST00000371953 NM_000314.4 291 gaa/gAaa 8/9 SUCCESS TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000025-T01-IM3 827 49 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000026-T01-IM3 261 370 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS PIK3CA GRCh37 3 178936094 178936094 + missense_variant Missense_Mutation SNP C C A rs121913286 P-0000026-T01-IM3 325 468 ENST00000263967.3:c.1636C>A p.Gln546Lys p.Q546K ENST00000263967 NM_006218.2 546 Cag/Aag 10/21 SUCCESS -LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000253339.5:c.1354C>G p.Pro452Ala p.P452A ENST00000253339 452 Cct/Gct 3/7 SUCCESS +LATS1 GRCh37 6 150004871 150004871 + missense_variant Missense_Mutation SNP G G C P-0000026-T01-IM3 716 109 ENST00000543571.1:c.1354C>G p.Pro452Ala p.P452A ENST00000543571 NM_004690.3 452 Cct/Gct 4/8 SUCCESS IKZF1 GRCh37 7 50467844 50467844 + missense_variant Missense_Mutation SNP G G A P-0000026-T01-IM3 469 135 ENST00000331340.3:c.1079G>A p.Arg360His p.R360H ENST00000331340 NM_006060.4 360 cGc/cAc 8/8 SUCCESS TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000027-T01-IM3 122 16 ENST00000310581 NM_198253.2 SUCCESS CUL3 GRCh37 2 225339012 225339012 + missense_variant Missense_Mutation SNP A A G P-0000039-T01-IM3 695 98 ENST00000264414.4:c.2257T>C p.Tyr753His p.Y753H ENST00000264414 NM_003590.4 753 Tat/Cat 16/16 SUCCESS @@ -59,21 +59,21 @@ BLM GRCh37 15 91292951 91292951 + missense_variant Missense_Mutation SNP C C G BLM GRCh37 15 91293024 91293024 + missense_variant Missense_Mutation SNP C C G P-0000034-T01-IM3 802 45 ENST00000355112.3:c.526C>G p.His176Asp p.H176D ENST00000355112 NM_000057.2 176 Cac/Gac 3/22 SUCCESS CIC GRCh37 19 42796756 42796756 + missense_variant Missense_Mutation SNP G G A rs781265178 P-0000034-T01-IM3 217 76 ENST00000575354.2:c.3214G>A p.Val1072Met p.V1072M ENST00000575354 NM_015125.3 1072 Gtg/Atg 14/20 SUCCESS KDM6A GRCh37 X 44969425 44969425 + frameshift_variant Frame_Shift_Del DEL G G - P-0000034-T01-IM3 239 284 ENST00000377967.4:c.4108del p.Glu1370LysfsTer6 p.E1370Kfs*6 ENST00000377967 NM_021140.2 1369 ttG/tt 28/29 SUCCESS -FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000318789.4:c.709A>G p.Ser237Gly p.S237G ENST00000318789 NM_032682.5 237 Agt/Ggt 11/21 SUCCESS -AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000349310.3:c.758A>G p.Tyr253Cys p.Y253C ENST00000349310 NM_001014432.1 253 tAt/tGt 10/15 SUCCESS +FOXP1 GRCh37 3 71090639 71090639 + missense_variant Missense_Mutation SNP T T C P-0000042-T01-IM3 459 232 ENST00000498215.1:c.709A>G p.Ser237Gly p.S237G ENST00000498215 NM_001244814.1 237 Agt/Ggt 7/17 SUCCESS +AKT1 GRCh37 14 105239862 105239862 + missense_variant Missense_Mutation SNP T T C rs751232562 P-0000047-T01-IM3 220 25 ENST00000407796.2:c.758A>G p.Tyr253Cys p.Y253C ENST00000407796 NM_001014431.1 253 tAt/tGt 9/14 SUCCESS BAP1 GRCh37 3 52443574 52443592 + frameshift_variant Frame_Shift_Del DEL GACATTTGCTCTGAAGGTC GACATTTGCTCTGAAGGTC - P-0000047-T01-IM3 241 201 ENST00000460680.1:c.100_118del p.Asp34ArgfsTer32 p.D34Rfs*32 ENST00000460680 NM_004656.3 34 GACCTTCAGAGCAAATGTCag/ag 3/17 SUCCESS TP53 GRCh37 17 7577120 7577120 + missense_variant Missense_Mutation SNP C C T rs28934576 P-0000055-T01-IM3 698 390 ENST00000269305.4:c.818G>A p.Arg273His p.R273H ENST00000269305 NM_001126112.2 273 cGt/cAt 8/11 SUCCESS NRAS GRCh37 1 115256510 115256510 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 580 195 ENST00000369535.4:c.201G>A p.Met67Ile p.M67I ENST00000369535 NM_002524.4 67 atG/atA 3/7 SUCCESS ATR GRCh37 3 142231242 142231242 + missense_variant Missense_Mutation SNP G G A P-0000055-T01-IM3 748 46 ENST00000350721.4:c.4712C>T p.Ser1571Phe p.S1571F ENST00000350721 NM_001184.3 1571 tCt/tTt 27/47 SUCCESS PIK3CA GRCh37 3 178916854 178916854 + missense_variant Missense_Mutation SNP G G A rs1057519929 P-0000055-T01-IM3 935 227 ENST00000263967.3:c.241G>A p.Glu81Lys p.E81K ENST00000263967 NM_006218.2 81 Gaa/Aaa 2/21 SUCCESS NOTCH3 GRCh37 19 15281521 15281521 + missense_variant Missense_Mutation SNP C C T P-0000055-T01-IM3 847 61 ENST00000263388.2:c.4852G>A p.Glu1618Lys p.E1618K ENST00000263388 NM_000435.2 1618 Gag/Aag 26/33 SUCCESS -PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000274335.5:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000274335 446 -/A 10/15 SUCCESS +PIK3R1 GRCh37 5 67589575 67589576 + frameshift_variant Frame_Shift_Ins INS - - A P-0000055-T01-IM3 742 207 ENST00000521381.1:c.1344dup p.Leu449IlefsTer3 p.L449Ifs*3 ENST00000521381 NM_181523.2 446 -/A 11/16 SUCCESS TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000056-T01-IM3 271 161 ENST00000310581 NM_198253.2 SUCCESS BAP1 GRCh37 3 52442579 52442579 + missense_variant Missense_Mutation SNP G G A rs1312611941 P-0000056-T01-IM3 617 328 ENST00000460680.1:c.166C>T p.Arg56Cys p.R56C ENST00000460680 NM_004656.3 56 Cgc/Tgc 4/17 SUCCESS FGFR4 GRCh37 5 176517519 176517519 + missense_variant Missense_Mutation SNP G G T P-0000056-T01-IM3 871 91 ENST00000292408.4:c.220G>T p.Ala74Ser p.A74S ENST00000292408 NM_213647.1 74 Gca/Tca 3/18 SUCCESS NOTCH4 GRCh37 6 32170183 32170183 + missense_variant Missense_Mutation SNP T T C P-0000056-T01-IM3 547 314 ENST00000375023.3:c.3425A>G p.Tyr1142Cys p.Y1142C ENST00000375023 NM_004557.3 1142 tAc/tGc 21/30 SUCCESS CDKN1A GRCh37 6 36652074 36652074 + stop_gained Nonsense_Mutation SNP G G T rs1213488369 P-0000056-T01-IM3 1248 88 ENST00000244741.5:c.196G>T p.Glu66Ter p.E66* ENST00000244741 NM_000389.4 66 Gag/Tag 2/3 SUCCESS -FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000260795.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000260795 370 gGc/gCACTc 8/17 SUCCESS +FGFR3 GRCh37 4 1806090 1806090 + protein_altering_variant In_Frame_Ins INS G G CACT P-0000056-T01-IM3 816 370 ENST00000440486.2:c.1109delinsCACT p.Gly370delinsAlaLeu p.G370delinsAL ENST00000440486 NM_000142.4 370 gGc/gCACTc 9/18 SUCCESS PIK3CA GRCh37 3 178936091 178936091 + missense_variant Missense_Mutation SNP G G A rs104886003 P-0000057-T01-IM3 389 132 ENST00000263967.3:c.1633G>A p.Glu545Lys p.E545K ENST00000263967 NM_006218.2 545 Gag/Aag 10/21 SUCCESS BARD1 GRCh37 2 215593578 215593578 + missense_variant Missense_Mutation SNP G G C P-0000057-T01-IM3 553 217 ENST00000260947.4:c.2156C>G p.Thr719Arg p.T719R ENST00000260947 NM_000465.2 719 aCa/aGa 11/11 SUCCESS MAP3K13 GRCh37 3 185198238 185198238 + missense_variant Missense_Mutation SNP C C T P-0000057-T01-IM3 461 262 ENST00000265026.3:c.2720C>T p.Ser907Phe p.S907F ENST00000265026 NM_004721.4 907 tCt/tTt 13/14 SUCCESS @@ -83,12 +83,12 @@ TP53 GRCh37 17 7578265 7578265 + missense_variant Missense_Mutation SNP A A G TP53 GRCh37 17 7577538 7577538 + missense_variant Missense_Mutation SNP C C T rs11540652 P-0000060-T01-IM3 162 217 ENST00000269305.4:c.743G>A p.Arg248Gln p.R248Q ENST00000269305 NM_001126112.2 248 cGg/cAg 7/11 SUCCESS PIK3CA GRCh37 3 178952085 178952085 + missense_variant Missense_Mutation SNP A A G rs121913279 P-0000060-T01-IM3 779 359 ENST00000263967.3:c.3140A>G p.His1047Arg p.H1047R ENST00000263967 NM_006218.2 1047 cAt/cGt 21/21 SUCCESS PTEN GRCh37 10 89717618 89717618 + missense_variant Missense_Mutation SNP T T C P-0000060-T01-IM3 634 106 ENST00000371953.3:c.643T>C p.Phe215Leu p.F215L ENST00000371953 NM_000314.4 215 Ttt/Ctt 7/9 SUCCESS -BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000380152.3:c.8632G>A p.Glu2878Lys p.E2878K ENST00000380152 2878 Gaa/Aaa 20/27 SUCCESS +BRCA2 GRCh37 13 32945237 32945237 + missense_variant,splice_region_variant Missense_Mutation SNP G G A rs398122710 P-0000060-T01-IM3 293 148 ENST00000544455.1:c.8632G>A p.Glu2878Lys p.E2878K ENST00000544455 NM_000059.3 2878 Gaa/Aaa 20/28 SUCCESS SMO GRCh37 7 128851867 128851867 + frameshift_variant,splice_region_variant Frame_Shift_Del DEL C C - P-0000060-T01-IM3 200 137 ENST00000249373.3:c.1943del p.Pro648GlnfsTer128 p.P648Qfs*128 ENST00000249373 NM_005631.4 647 Ccc/cc 12/12 SUCCESS MCL1 GRCh37 1 150551364 150551381 + frameshift_variant Frame_Shift_Del DEL GTCGTAAGGTCTCCAGCG GTCGTAAGGTCTCCAGCG ATCC P-0000060-T01-IM3 1561 122 ENST00000369026.2:c.626_643delinsGGAT p.Ala209GlyfsTer63 p.A209Gfs*63 ENST00000369026 NM_021960.4 209 gCGCTGGAGACCTTACGACgg/gGGATgg 1/3 SUCCESS PIK3CA GRCh37 3 178952090 178952090 + missense_variant Missense_Mutation SNP G G C rs121913277 P-0000061-T01-IM3 762 155 ENST00000263967.3:c.3145G>C p.Gly1049Arg p.G1049R ENST00000263967 NM_006218.2 1049 Ggt/Cgt 21/21 SUCCESS FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 765 173 ENST00000441802.2:c.7771G>C p.Asp2591His p.D2591H ENST00000441802 NM_005245.3 2591 Gac/Cac 10/27 SUCCESS -SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS +SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000358026.2:c.3727C>G p.Arg1243Gly p.R1243G ENST00000358026 NM_001128849.1 1243 Cgg/Ggg 26/36 SUCCESS TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000320356.2:c.848C>T p.Thr283Met p.T283M ENST00000320356 NM_004456.4 283 aCg/aTg 8/20 SUCCESS MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS @@ -97,6 +97,6 @@ KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS TERT GRCh37 5 1295228 1295228 + upstream_gene_variant 5'Flank SNP G G A rs1242535815 P-0000063-T01-IM3 18 79 ENST00000310581 NM_198253.2 SUCCESS EPHB1 GRCh37 3 134670264 134670264 + stop_gained Nonsense_Mutation SNP C C T rs750670511 P-0000063-T01-IM3 540 220 ENST00000398015.3:c.175C>T p.Gln59Ter p.Q59* ENST00000398015 NM_004441.4 59 Cag/Tag 3/16 SUCCESS -FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000260795.2:c.1244C>T p.Ser415Phe p.S415F ENST00000260795 415 tCc/tTc 8/17 SUCCESS +FGFR3 GRCh37 4 1806225 1806225 + missense_variant Missense_Mutation SNP C C T P-0000063-T01-IM3 286 194 ENST00000440486.2:c.1244C>T p.Ser415Phe p.S415F ENST00000440486 NM_000142.4 415 tCc/tTc 9/18 SUCCESS FAT1 GRCh37 4 187518888 187518888 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 298 375 ENST00000441802.2:c.12316G>C p.Asp4106His p.D4106H ENST00000441802 NM_005245.3 4106 Gac/Cac 24/27 SUCCESS FAT1 GRCh37 4 187518921 187518921 + missense_variant Missense_Mutation SNP C C G P-0000063-T01-IM3 252 317 ENST00000441802.2:c.12283G>C p.Asp4095His p.D4095H ENST00000441802 NM_005245.3 4095 Gat/Cat 24/27 SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.uniprot.nucleotide_context.txt b/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.uniprot.nucleotide_context.txt index db2692ab..e92ddf86 100644 --- a/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.uniprot.nucleotide_context.txt +++ b/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.uniprot.nucleotide_context.txt @@ -1,4 +1,4 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT +#genome_nexus_version: 1.0.2 #isoform: uniprot Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence 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 t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Ref_Tri Var_Tri Annotation_Status SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 CAT CTT SUCCESS @@ -91,7 +91,7 @@ FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 GCG GGG SUCCESS TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 CGG CAG SUCCESS EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 CGT CAT SUCCESS -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 GAG GTG SUCCESS +MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000258149.5:c.446A>T p.Glu149Val p.E149V ENST00000258149 NM_001145339.2 149 gAg/gTg 6/9 GAG GTG SUCCESS IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 ATT AGT SUCCESS KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 AGA ACA SUCCESS KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 GGA GCA SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.uniprot.txt b/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.uniprot.txt index a8482108..b9fcab5a 100644 --- a/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.uniprot.txt +++ b/annotationPipeline/src/test/resources/expected/data_mutations_extended_100.uniprot.txt @@ -1,4 +1,4 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT +#genome_nexus_version: 1.0.2 #isoform: uniprot Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence 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 t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status SPEN GRCh37 1 16265908 16265908 + missense_variant Missense_Mutation SNP A A T P-0000004-T01-IM3 400 73 ENST00000375759.3:c.10981A>T p.Ile3661Phe p.I3661F ENST00000375759 NM_015001.2 3661 Att/Ttt 15/15 SUCCESS @@ -91,7 +91,7 @@ FAT1 GRCh37 4 187539969 187539969 + missense_variant Missense_Mutation SNP C C SMARCA4 GRCh37 19 11144146 11144146 + missense_variant Missense_Mutation SNP C C G P-0000061-T01-IM3 205 81 ENST00000344626.4:c.3727C>G p.Arg1243Gly p.R1243G ENST00000344626 NM_003072.3 1243 Cgg/Ggg 26/35 SUCCESS TP53 GRCh37 17 7577539 7577539 + missense_variant Missense_Mutation SNP G G A rs121912651 P-0000062-T01-IM3 265 581 ENST00000269305.4:c.742C>T p.Arg248Trp p.R248W ENST00000269305 NM_001126112.2 248 Cgg/Tgg 7/11 SUCCESS EZH2 GRCh37 7 148523605 148523605 + missense_variant Missense_Mutation SNP G G A rs587778304 P-0000062-T01-IM3 980 54 ENST00000460911.1:c.848C>T p.Thr283Met p.T283M ENST00000460911 283 aCg/aTg 8/20 SUCCESS -MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000462284.1:c.629A>T p.Glu210Val p.E210V ENST00000462284 NM_002392.5 210 gAg/gTg 8/11 SUCCESS +MDM2 GRCh37 12 69222656 69222656 + missense_variant Missense_Mutation SNP A A T P-0000062-T01-IM3 1485 328 ENST00000258149.5:c.446A>T p.Glu149Val p.E149V ENST00000258149 NM_001145339.2 149 gAg/gTg 6/9 SUCCESS IGF1R GRCh37 15 99486153 99486153 + missense_variant,splice_region_variant Missense_Mutation SNP T T G P-0000062-T01-IM3 927 69 ENST00000268035.6:c.3459T>G p.Asp1153Glu p.D1153E ENST00000268035 NM_000875.3 1153 gaT/gaG 19/21 SUCCESS KEAP1 GRCh37 19 10602303 10602303 + missense_variant Missense_Mutation SNP G G C rs754011905 P-0000062-T01-IM3 807 422 ENST00000171111.5:c.1275C>G p.Ile425Met p.I425M ENST00000171111 NM_203500.1 425 atC/atG 3/6 SUCCESS KDM5C GRCh37 X 53223386 53223386 + missense_variant Missense_Mutation SNP G G C P-0000062-T01-IM3 514 151 ENST00000375401.3:c.3973C>G p.Pro1325Ala p.P1325A ENST00000375401 NM_004187.3 1325 Cct/Gct 23/26 SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/minimal_example.uniprot.txt b/annotationPipeline/src/test/resources/expected/minimal_example.uniprot.txt index 6d3ee305..6d114d38 100644 --- a/annotationPipeline/src/test/resources/expected/minimal_example.uniprot.txt +++ b/annotationPipeline/src/test/resources/expected/minimal_example.uniprot.txt @@ -1,4 +1,4 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT +#genome_nexus_version: 1.0.2 #isoform: uniprot Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence 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 t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number Annotation_Status PIK3CA 5290 GRCh37 3 178916927 178916939 + protein_altering_variant In_Frame_Del DEL TAGGCAACCGTGA G G ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG ENST00000263967 NM_006218.2 105 gTAGGCAACCGTGAa/gGa 2/21 SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/my_variant_info_corner_cases.uniprot.txt b/annotationPipeline/src/test/resources/expected/my_variant_info_corner_cases.uniprot.txt index 336c3387..9c69a1bc 100644 --- a/annotationPipeline/src/test/resources/expected/my_variant_info_corner_cases.uniprot.txt +++ b/annotationPipeline/src/test/resources/expected/my_variant_info_corner_cases.uniprot.txt @@ -1,4 +1,4 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT +#genome_nexus_version: 1.0.2 #isoform: uniprot Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence 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 t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF gnomAD_SAS_AF Annotation_Status -BARD1 580 GRCh37 2 215645503 215645523 + inframe_deletion In_Frame_Del DEL TGGTGAAGAACATTCAGGCAA - - rs28997575 ENST00000260947.4:c.1075_1095del p.Leu359_Pro365del p.L359_P365del ENST00000260947 NM_000465.2 359 TTGCCTGAATGTTCTTCACCA/- 4/11 0.0288928 0.0431947 0.0336575 0.012004 0.0438969 0.00355757 0.0178879 0.0324421 0.0705371 SUCCESS +BARD1 580 GRCh37 2 215645503 215645523 + inframe_deletion In_Frame_Del DEL TGGTGAAGAACATTCAGGCAA - - rs28997575 ENST00000260947.4:c.1075_1095del p.Leu359_Pro365del p.L359_P365del ENST00000260947 NM_000465.2 359 TTGCCTGAATGTTCTTCACCA/- 4/11 SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/test_output_format_extended.expected.txt b/annotationPipeline/src/test/resources/expected/test_output_format_extended.expected.txt index 5d7903dc..c9e6cb0a 100644 --- a/annotationPipeline/src/test/resources/expected/test_output_format_extended.expected.txt +++ b/annotationPipeline/src/test/resources/expected/test_output_format_extended.expected.txt @@ -1,4 +1,4 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT +#genome_nexus_version: 1.0.2 #isoform: uniprot Hugo_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 HGVSp_Short t_alt_count t_ref_count n_alt_count n_ref_count A B C Codons Consequence D Exon_Number HGVSc HGVSp Protein_position RefSeq Transcript_ID Annotation_Status PIK3CA 5290 GRCh37 3 178916927 178916939 + In_Frame_Del DEL TAGGCAACCGTGA G G p.V105_E109delinsG gTAGGCAACCGTGAa/gGa protein_altering_variant 2/21 ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly 105 NM_006218.2 ENST00000263967 SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/test_output_format_minimal.expected.txt b/annotationPipeline/src/test/resources/expected/test_output_format_minimal.expected.txt index 234a971b..313f781e 100644 --- a/annotationPipeline/src/test/resources/expected/test_output_format_minimal.expected.txt +++ b/annotationPipeline/src/test/resources/expected/test_output_format_minimal.expected.txt @@ -1,4 +1,4 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT +#genome_nexus_version: 1.0.2 #isoform: uniprot Chromosome Start_Position End_Position Reference_Allele Tumor_Seq_Allele1 BAM_File Center Codons Consequence Entrez_Gene_Id Exon_Number HGVSc HGVSp HGVSp_Short Hugo_Symbol Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Match_Norm_Validation_Allele1 Match_Norm_Validation_Allele2 Matched_Norm_Sample_Barcode Mutation_Status NCBI_Build Protein_position RefSeq Score Sequence_Source Sequencer Sequencing_Phase Strand Transcript_ID Tumor_Sample_Barcode Tumor_Seq_Allele2 Tumor_Validation_Allele1 Tumor_Validation_Allele2 Validation_Method Validation_Status Variant_Classification Variant_Type Verification_Status dbSNP_RS dbSNP_Val_Status n_alt_count n_ref_count t_alt_count t_ref_count Annotation_Status 3 178916927 178916939 TAGGCAACCGTGA G gTAGGCAACCGTGAa/gGa protein_altering_variant 5290 2/21 ENST00000263967.3:c.314_326delinsG p.Val105_Glu109delinsGly p.V105_E109delinsG PIK3CA GRCh37 105 NM_006218.2 + ENST00000263967 G In_Frame_Del DEL SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/test_output_format_with_formatFile.expected.txt b/annotationPipeline/src/test/resources/expected/test_output_format_with_formatFile.expected.txt index 89244e6b..bffca635 100644 --- a/annotationPipeline/src/test/resources/expected/test_output_format_with_formatFile.expected.txt +++ b/annotationPipeline/src/test/resources/expected/test_output_format_with_formatFile.expected.txt @@ -1,4 +1,4 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT +#genome_nexus_version: 1.0.2 #isoform: uniprot Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Annotation_Status SPEN 23013 GRCh37 1 SUCCESS diff --git a/annotationPipeline/src/test/resources/expected/vcf2maf_tests.mskcc.txt b/annotationPipeline/src/test/resources/expected/vcf2maf_tests.mskcc.txt index 3398ba55..1863e890 100644 --- a/annotationPipeline/src/test/resources/expected/vcf2maf_tests.mskcc.txt +++ b/annotationPipeline/src/test/resources/expected/vcf2maf_tests.mskcc.txt @@ -1,4 +1,4 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT +#genome_nexus_version: 1.0.2 #isoform: mskcc #version 2.4 Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence 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 t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number n_depth t_depth Annotation_Status diff --git a/annotationPipeline/src/test/resources/expected/vcf2maf_tests.uniprot.txt b/annotationPipeline/src/test/resources/expected/vcf2maf_tests.uniprot.txt index bbbfc848..7f7fea69 100644 --- a/annotationPipeline/src/test/resources/expected/vcf2maf_tests.uniprot.txt +++ b/annotationPipeline/src/test/resources/expected/vcf2maf_tests.uniprot.txt @@ -1,4 +1,4 @@ -#genome_nexus_version: 0-unknown-version-SNAPSHOT +#genome_nexus_version: 1.0.2 #isoform: uniprot #version 2.4 Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position End_Position Strand Consequence 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 t_ref_count t_alt_count n_ref_count n_alt_count HGVSc HGVSp HGVSp_Short Transcript_ID RefSeq Protein_position Codons Exon_Number n_depth t_depth Annotation_Status diff --git a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java index 2f4e1a55..2f829232 100644 --- a/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java +++ b/annotator/src/main/java/org/cbioportal/annotator/internal/GenomeNexusImpl.java @@ -192,8 +192,8 @@ public List annotateRecordsUsingGET(AnnotationSummaryStatistics public String getVersion() { InfoControllerApi infoApiClient = new InfoControllerApi(); try { - Version result = infoApiClient.fetchVersionGET(); - return result.getVersion(); + AggregateSourceInfo result = infoApiClient.fetchVersionGET(); + return result.getGenomeNexus().getServer().getVersion(); } catch (ApiException e) { LOG.error("Exception when calling InfoControllerApi#fetchVersionGET, genome nexus version is unknown", e); } diff --git a/pom.xml b/pom.xml index 50a6f6e9..883e183f 100644 --- a/pom.xml +++ b/pom.xml @@ -103,12 +103,12 @@ com.github.genome-nexus.genome-nexus-java-api-client genomeNexusPublicApiClient - 600501017ef64be14cfb36679babec30da9200ca + 59f677151e77710be41ff07ac92969d383287068 com.github.genome-nexus.genome-nexus-java-api-client genomeNexusInternalApiClient - 600501017ef64be14cfb36679babec30da9200ca + 59f677151e77710be41ff07ac92969d383287068 org.mockito