From a8dfabf58e56889ab10e3a1f7313548c349620f8 Mon Sep 17 00:00:00 2001 From: averyniceday Date: Mon, 12 Dec 2022 13:51:24 -0800 Subject: [PATCH] update GNAP to use updated schema - (InfoControllerApi updated to return multiple versions such as GN server, database, VEP...) (#236) Version outputted will be GN Server Version Updated header in expected outputs for integration tests Updated unit tests to reflect actual output from GN (these tests are brittle and unrelated to the version change, will most likely break down the line) Co-authored-by: Avery Wang --- .../resources/expected/corner_cases.mskcc.txt | 2 +- ...orner_cases.two_tumor_seq_allele.mskcc.txt | 2 +- ...ner_cases.two_tumor_seq_allele.uniprot.txt | 2 +- .../expected/corner_cases.uniprot.txt | 2 +- .../data_mutations_extended_100.mskcc.txt | 34 +++++++++---------- ...xtended_100.uniprot.nucleotide_context.txt | 4 +-- .../data_mutations_extended_100.uniprot.txt | 4 +-- .../expected/minimal_example.uniprot.txt | 2 +- .../my_variant_info_corner_cases.uniprot.txt | 4 +-- .../test_output_format_extended.expected.txt | 2 +- .../test_output_format_minimal.expected.txt | 2 +- ...output_format_with_formatFile.expected.txt | 2 +- .../expected/vcf2maf_tests.mskcc.txt | 2 +- .../expected/vcf2maf_tests.uniprot.txt | 2 +- .../annotator/internal/GenomeNexusImpl.java | 4 +-- pom.xml | 4 +-- 16 files changed, 37 insertions(+), 37 deletions(-) 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