public void MissingClinvarId()
{
JsonUtilities.AlleleContains("1 55518316 rs2483205 C T . . RS=2483205;RSPOS=55518316",
Resources.MiniSuppAnnot("chr1_55518316_55518317.nsa"),
"\"clinVar\":[{\"id\":\"RCV000030351.1\",\"reviewStatus\":\"criteria provided, single submitter\",\"isAlleleSpecific\":true,\"alleleOrigins\":[\"not provided\"],\"refAllele\":\"C\",\"altAllele\":\"T\",\"phenotypes\":[\"Familial hypercholesterolemia\"],\"medGenIDs\":[\"C0020445\"],\"omimIDs\":[\"143890\"],\"orphanetIDs\":[\"391665\"],\"significance\":\"benign\",\"lastUpdatedDate\":\"2016-08-29\",\"pubMedIds\":[\"12730697\",\"17094996\"]}]"
);
}
public void ClinVarIndel2()
{
JsonUtilities.AlleleContains(
"chr9 134385435 . C T . . .",
Resources.MiniSuppAnnot("chr9_134385435_134385435.nsa"),
"{\"id\":\"RCV000223329.1\",\"reviewStatus\":\"criteria provided, single submitter\",\"alleleOrigins\":[\"germline\"],\"refAllele\":\"CA\",\"altAllele\":\"TG\",\"phenotypes\":[\"not specified\"],\"medGenIDs\":[\"CN169374\"],\"significance\":\"benign\",\"lastUpdatedDate\":\"2016-08-26\",\"pubMedIds\":[\"24033266\"]}");
}
public void ClinVarAnnotateCrash()
{
JsonUtilities.AlleleContains(
"13 111335401 . GCTC G 0 . . .",
Resources.MiniSuppAnnot("chr13_111335401_111335402.nsa"),
"clinVar");
}
public void ClinVarIndel()
{
JsonUtilities.AlleleContains(
"chr4 186201148 . ATCATACAGGTCATCGCT AGC . . .",
Resources.MiniSuppAnnotGRCh38("chr4_186201148_186201149.nsa"),
"{\"id\":\"RCV000032548.5\",\"reviewStatus\":\"no assertion criteria provided\",\"isAlleleSpecific\":true,\"alleleOrigins\":[\"not provided\",\"germline\"],\"refAllele\":\"TCATACAGGTCATCGCT\",\"altAllele\":\"GC\",\"phenotypes\":[\"Bietti crystalline corneoretinal dystrophy\"],\"medGenIDs\":[\"C1859486\"],\"omimIDs\":[\"210370\"],\"significance\":\"pathogenic\",\"lastUpdatedDate\":\"2016-08-29\",\"pubMedIds\":[\"15042513\",\"15937078\",\"22693542\",\"23661369\"]}");
}
public void CosmicAlleleContains()
{
JsonUtilities.AlleleContains(
"1 898602 COSM2151955 GCG G . . GENE=KLHL17;STRAND=+;CDS=c.1157_1158delCG;AA=p.A386fs*12;CNT=1",
Resources.MiniSuppAnnot("chr1_898602_898603.nsa"),
"\"cosmic\":[{\"id\":\"COSM2150687\",\"refAllele\":\"C\",\"altAllele\":\"G\",\"gene\":\"KLHL17\",\"sampleCount\":1,\"studies\":[{\"histology\":\"glioma\",\"primarySite\":\"central nervous system\"}]},{\"id\":\"COSM2151955\",\"isAlleleSpecific\":true,\"refAllele\":\"CG\",\"altAllele\":\"-\",\"gene\":\"KLHL17\",\"sampleCount\":1,\"studies\":[{\"histology\":\"glioma\",\"primarySite\":\"central nervous system\"}]}]");
}
public void ClinvarAlleleOrigin()
{
JsonUtilities.AlleleContains(
"9 120475302 . A G 156.00 PASS SNVSB=-21.8;SNVHPOL=2 GT:GQ:GQX:DP:DPF:AD 0/1:169:155:27:0:13,14",
Resources.MiniSuppAnnot("chr9_120475302_120475303.nsa"),
"\"clinVar\":[{\"id\":\"RCV000007040.4\",\"reviewStatus\":\"no assertion criteria provided\",\"isAlleleSpecific\":true,\"alleleOrigins\":[\"germline\"],\"refAllele\":\"A\",\"altAllele\":\"G\",\"phenotypes\":[\"TLR4 POLYMORPHISM\"],\"significance\":\"benign\",\"lastUpdatedDate\":\"2016-08-26\",\"pubMedIds\":[\"10835634\",\"12124407\",\"15547160\",\"15829498\",\"16879199\",\"17704786\"]}]");
}
public void AlleleSpecificFlagFalse()
{
JsonUtilities.AlleleContains(
"chr1 118165691 rs1630312 C T 156.00 PASS SNVSB=-21.8;SNVHPOL=2;AF=0.25;EVS=0.3063|85.0|6503;GMAF=T|0.2523;phastCons;CSQT=FAM46C|NM_017709.3|synonymous_variant GT:GQ:GQX:DP:DPF:AD 0/1:169:155:27:0:13,14",
Resources.MiniSuppAnnot("chr1_118165691_118165692.nsa"),
"\"cosmic\":[{\"id\":\"COSM3750276\",\"isAlleleSpecific\":true,\"refAllele\":\"C\",\"altAllele\":\"T\",\"gene\":\"FAM46C\",\"sampleCount\":2");
}
public void CosmicAlleleSpecificFlag()
{
JsonUtilities.AlleleContains(
"chr1 565591 rs7416152 C T 39.00 PASS SNVSB=-4.1;SNVHPOL=4;cosmic=COSN210317 GT:GQ:GQX:DP:DPF:AD 0/1:72:39:37:1:30,7",
Resources.MiniSuppAnnot("chr1_565591_565592.nsa"),
"\"cosmic\":[{\"id\":\"COSN210317\",\"isAlleleSpecific\":true,\"refAllele\":\"C\",\"altAllele\":\"T\"}]");
}
public void MissingRsid()
{
JsonUtilities.AlleleContains(
"chr1 129010 rs377161483 AATG A 32 LowGQXHetAltDel CIGAR=1M1D1M,2M1D;RU=C,A;REFREP=1,17;IDREP=0,16 GT:GQ:GQX:DPI:AD 1/2:162:2:22:4,8,1",
Resources.MiniSuppAnnot("chr1_129010_129012.nsa"),
"{\"altAllele\":\"-\",\"refAllele\":\"ATG\",\"begin\":129011,\"chromosome\":\"chr1\",\"dbsnp\":[\"rs377161483\"],\"end\":129013,\"variantType\":\"deletion\",\"vid\":\"1:129011:129013\"");
}
public void CosmicLongDelInsAlleleError()
{
JsonUtilities.AlleleContains(
"chr18 58484430 . AAT A 39.00 PASS SNVSB=-4.1;SNVHPOL=4 GT:GQ:GQX:DP:DPF:AD 0/1:72:39:37:1:30,7",
Resources.MiniSuppAnnot("chr18_58484430_58484431.nsa"),
"\"cosmic\":[{\"id\":\"COSN197004\",\"refAllele\":\"ATGTGAAAAATATATTTTATATAATTTCAATATTTTTAACA\",\"altAllele\":\"TTGAAAAATATATTTTATATAATTTCAATATTTTTAACAT\"}]");
}
public void CosmicMissingStudy()
{
JsonUtilities.AlleleContains(
"chr2 203066048 . G T 39.00 PASS SNVSB=-4.1;SNVHPOL=4 GT:GQ:GQX:DP:DPF:AD 0/1:72:39:37:1:30,7",
Resources.MiniSuppAnnot("chr2_203066046_203066050.nsa"),
"\"cosmic\":[{\"id\":\"COSN166383\",\"isAlleleSpecific\":true,\"refAllele\":\"G\",\"altAllele\":\"T\"}]");
}
public void MissingCosmicNonCoding()
{
JsonUtilities.AlleleContains(
"2 203066048 rs12693962 G T . LowQscore SOMATIC;QSS=1;TQSS=1;NT=het;QSS_NT=1;TQSS_NT=1;SGT=GT->GT;DP=150;MQ=59.50;MQ0=2;ALTPOS=50;ALTMAP=23;ReadPosRankSum=0.18;SNVSB=0.00;PNOISE=0.00;PNOISE2=0.00;VQSR=0.00;AA=G;AF1000G=0.235823;phyloP=2.166;CSQT=1|DAZAP2P1|ENST00000475212|downstream_gene_variant,1|SUMO1|ENST00000392246|downstream_gene_variant DP:FDP:SDP:SUBDP:AU:CU:GU:TU 55:1:0:0:0,0:0,0:34,35:20,20 91:1:0:0:0,0:0,0:71,72:19,19",
Resources.MiniSuppAnnot("chr2_203066048_203066049.nsa"),
"{\"ancestralAllele\":\"G\",\"altAllele\":\"T\",\"refAllele\":\"G\",\"begin\":203066048,\"chromosome\":\"2\",\"dbsnp\":[\"rs12693962\"],\"end\":203066048,\"globalMinorAllele\":\"T\",\"gmaf\":0.2358,\"variantType\":\"SNV\",\"vid\":\"2:203066048:T\",\"cosmic\":[{\"id\":\"COSN166383\",\"isAlleleSpecific\":true,\"refAllele\":\"G\",\"altAllele\":\"T\"}]");
}
public void AlleleSpecificCosmic()
{
JsonUtilities.AlleleContains(
"chr1 111783982 rs1630312 C A 156.00 PASS SNVSB=-21.8;SNVHPOL=2 GT:GQ:GQX:DP:DPF:AD 0/1:169:155:27:0:13,14",
Resources.MiniSuppAnnot("chr1_111783982_111783983.nsa"), "\"id\":\"COSM3996742\",\"isAlleleSpecific\":true,\"refAllele\":\"C\",\"altAllele\":\"A\",\"gene\":\"CHI3L2\",\"sampleCount\":1");
JsonUtilities.AlleleContains(
"chr1 111783982 rs1630312 C A 156.00 PASS SNVSB=-21.8;SNVHPOL=2 GT:GQ:GQX:DP:DPF:AD 0/1:169:155:27:0:13,14",
Resources.MiniSuppAnnot("chr1_111783982_111783983.nsa"), "{\"id\":544,\"histology\":\"haematopoietic neoplasm\",\"primarySite\":\"haematopoietic and lymphoid tissue\"}");
JsonUtilities.AlleleContains(
"chr1 111783982 rs1630312 C A 156.00 PASS SNVSB=-21.8;SNVHPOL=2 GT:GQ:GQX:DP:DPF:AD 0/1:169:155:27:0:13,14",
Resources.MiniSuppAnnot("chr1_111783982_111783983.nsa"), "\"id\":\"COSM4591038\",\"refAllele\":\"C\",\"altAllele\":\"T\",\"gene\":\"CHI3L2\",\"sampleCount\":4");
JsonUtilities.AlleleContains(
"chr1 111783982 rs1630312 C A 156.00 PASS SNVSB=-21.8;SNVHPOL=2 GT:GQ:GQX:DP:DPF:AD 0/1:169:155:27:0:13,14",
Resources.MiniSuppAnnot("chr1_111783982_111783983.nsa"), "{\"histology\":\"lymphoid neoplasm\",\"primarySite\":\"haematopoietic and lymphoid tissue\"}");
JsonUtilities.AlleleContains(
"chr1 111783982 rs1630312 C A 156.00 PASS SNVSB=-21.8;SNVHPOL=2 GT:GQ:GQX:DP:DPF:AD 0/1:169:155:27:0:13,14",
Resources.MiniSuppAnnot("chr1_111783982_111783983.nsa"), "{\"histology\":\"carcinoma\",\"primarySite\":\"upper aerodigestive tract\"}");
JsonUtilities.AlleleContains(
"chr1 111783982 rs1630312 C A 156.00 PASS SNVSB=-21.8;SNVHPOL=2 GT:GQ:GQX:DP:DPF:AD 0/1:169:155:27:0:13,14",
Resources.MiniSuppAnnot("chr1_111783982_111783983.nsa"), "{\"histology\":\"osteosarcoma\",\"primarySite\":\"bone\"}");
}
public void TrimClinvarAllele()
{
// 13 40298638 rs66629036 TA T . . RS=66629036;RSPOS=40298641;dbSNPBuildID=134;SSR=0;SAO=0;VP=0x050000080005000002000200;GENEINFO=COG6:57511;WGT=1;VC=DIV;INT;ASP;CLNALLE=1;CLNHGVS=NC_000013.10:g.40298641delA;CLNSRC=.;CLNORIGIN=1;CLNSRCID=.;CLNSIG=2;CLNDSDB=MedGen;CLNDSDBID=CN169374;CLNDBN=not_specified;CLNREVSTAT=single;CLNACC=RCV000082045.4
JsonUtilities.AlleleContains(
"13 40298637 rs66629036 TTA TT . . PASS RefMinor;GMAF=T|0.01877 GT:GQX:DP:DPF:AD 0/0:69:24:3:24",
Resources.MiniSuppAnnot("chr13_40298638_40298639.nsa"),
"{\"id\":\"RCV000082045.4\",\"reviewStatus\":\"criteria provided, single submitter\",\"isAlleleSpecific\":true,\"alleleOrigins\":[\"germline\"],\"refAllele\":\"A\",\"altAllele\":\"-\",\"phenotypes\":[\"not specified\"],\"medGenIDs\":[\"CN169374\"],\"significance\":\"benign\",\"lastUpdatedDate\":\"2016-08-26\",\"pubMedIds\":[\"23757202\"]}");
}
public void ClinVarAltAllele()
{
JsonUtilities.AlleleContains(
"1 9305316 rs398122818 AC A . . RS=398122818;RSPOS=9305318;dbSNPBuildID=138;SSR=0;SAO=0;VP=0x050060001205000002110200;GENEINFO=H",
Resources.MiniSuppAnnot("chr1_9305316_9305317.nsa"),
"\"clinVar\":[{\"id\":\"RCV000024293.28\",\"reviewStatus\":\"no assertion criteria provided\",\"isAlleleSpecific\":true,\"alleleOrigins\":[\"germline\"],\"refAllele\":\"C\",\"altAllele\":\"-\",\"phenotypes\":[\"Cortisone reductase deficiency 1\"],\"medGenIDs\":[\"C3551716\"],\"omimIDs\":[\"604931\"],\"orphanetIDs\":[\"168588\"],\"significance\":\"pathogenic\",\"lastUpdatedDate\":\"2016-08-26\",\"pubMedIds\":[\"11150889\",\"18628520\"]}]"
);
}
public void CarryOverDbsnp()
{
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, Resources.MiniSuppAnnot("chr2_118565152_118565155.nsa"),
"2 118565152 . AGC AGT,CGC 50 PASS SNVSB=-8.7;SNVHPOL=5;CSQ=AGT|upstream_gene_variant|MODIFIER|AC009312.1|ENSG00000238207|Transcript|ENST00000457110|antisense|||||||||||3402|-1|Clone_based_vega_gene||YES|||||||||,CGC|upstream_gene_variant|MODIFIER|AC009312.1|ENSG00000238207|Transcript|ENST00000457110|antisense|||||||||||3402|-1|Clone_based_vega_gene||YES||||||||| GT:GQ:GQX:DP:DPF:AD 1/2:83:21:12:2:0,8,4");
Assert.NotNull(annotatedVariant);
JsonUtilities.AlleleContains(annotatedVariant,
"{\"altAllele\":\"T\",\"refAllele\":\"C\",\"begin\":118565154,\"chromosome\":\"2\",\"dbsnp\":[\"rs62192625\",\"rs77494680\"],\"end\":118565154,\"globalMinorAllele\":\"T\",\"gmaf\":0.3464,\"variantType\":\"SNV\",\"vid\":\"2:118565154:T");
JsonUtilities.AlleleEquals(annotatedVariant,
"{\"altAllele\":\"C\",\"refAllele\":\"A\",\"begin\":118565152,\"chromosome\":\"2\",\"dbsnp\":[\"rs754609911\"],\"end\":118565152,\"variantType\":\"SNV\",\"vid\":\"2:118565152:C\"}",
1);
}
public void UniqueCosmicStudy()
{
JsonUtilities.AlleleContains(
"17 1183338 . C T 97 PASS SNVSB=-13.0;SNVHPOL=2;CSQ=T|ENSG00000184811|ENST00000333813|Transcript|missense_variant|382|43|15|P/S|Cca/Tca||||1/3||ENST00000333813.3:c.43C>T|ENSP00000329548.3:p.Pro15Ser|ENSP00000329548|benign(0.213)|YES|tolerated(0.13)||||||TUSC5|CCDS42225.1 GT:GQ:GQX:DP:DPF:AD 0/1:96:93:17:0:7,10",
Resources.MiniSuppAnnot("chr17_1183338_1183339.nsa"),
"{\"id\":\"COSM4129566\",\"isAlleleSpecific\":true,\"refAllele\":\"C\",\"altAllele\":\"T\",\"gene\":\"TUSC5\",\"sampleCount\":4");
JsonUtilities.AlleleContains(
"17 1183338 . C T 97 PASS SNVSB=-13.0;SNVHPOL=2;CSQ=T|ENSG00000184811|ENST00000333813|Transcript|missense_variant|382|43|15|P/S|Cca/Tca||||1/3||ENST00000333813.3:c.43C>T|ENSP00000329548.3:p.Pro15Ser|ENSP00000329548|benign(0.213)|YES|tolerated(0.13)||||||TUSC5|CCDS42225.1 GT:GQ:GQX:DP:DPF:AD 0/1:96:93:17:0:7,10",
Resources.MiniSuppAnnot("chr17_1183338_1183339.nsa"),
"{\"id\":544,\"histology\":\"haematopoietic neoplasm\",\"primarySite\":\"haematopoietic and lymphoid tissue\"}");
JsonUtilities.AlleleContains(
"17 1183338 . C T 97 PASS SNVSB=-13.0;SNVHPOL=2;CSQ=T|ENSG00000184811|ENST00000333813|Transcript|missense_variant|382|43|15|P/S|Cca/Tca||||1/3||ENST00000333813.3:c.43C>T|ENSP00000329548.3:p.Pro15Ser|ENSP00000329548|benign(0.213)|YES|tolerated(0.13)||||||TUSC5|CCDS42225.1 GT:GQ:GQX:DP:DPF:AD 0/1:96:93:17:0:7,10",
Resources.MiniSuppAnnot("chr17_1183338_1183339.nsa"),
"{\"id\":589,\"histology\":\"other\",\"primarySite\":\"thyroid\"}");
}
public void ClinVarNonEnglishChars()
{
JsonUtilities.AlleleContains("1 225592187 . CTAGAAGA CCTTCTAG 362 PASS CIGAR=1M18D",
Resources.MiniSuppAnnot("chr1_225592187_225592188.nsa"),
"Pelger-Huët anomaly");
}
public void CosmicTsvChrXname23()
{
JsonUtilities.AlleleContains("X 2856155 COSM5003595 C T . . GENE=ARSE", Resources.MiniSuppAnnot("chrX_2856155_2856156.nsa"),
"\"cosmic\":[{\"id\":\"COSM5003595\",\"isAlleleSpecific\":true,\"refAllele\":\"C\",\"altAllele\":\"T\",\"gene\":\"ARSE\",\"sampleCount\":1,\"studies\":[{\"histology\":\"carcinoma\",\"primarySite\":\"pancreas\"}]},{\"id\":\"COSM5003596\",\"isAlleleSpecific\":true,\"refAllele\":\"C\",\"altAllele\":\"T\",\"gene\":\"ARSE_ENST00000540563\",\"sampleCount\":1,\"studies\":[{\"histology\":\"carcinoma\",\"primarySite\":\"pancreas\"}]}]");
}
public void CosmicInsDel()
{
JsonUtilities.AlleleContains(
"3 10188320 COSM18152 G A . . GENE=VHL;STRAND=+;CDS=c.463G>A;AA=p.V155M;CNT=7",
Resources.MiniSuppAnnot("chr3_10188320_10188321.nsa"), "\"id\":\"COSM14426\",\"refAllele\":\"GGTACTGAC\",\"altAllele\":\"A\"");
}
public void MissingCosmicStudies()
{
JsonUtilities.AlleleContains("19 33792363 COSM249867 CACTGGTC C . . .", Resources.MiniSuppAnnot("chr19_33792363_33792364.nsa"),
"{\"id\":\"COSM249867\",\"isAlleleSpecific\":true,\"refAllele\":\"ACTGGTC\",\"altAllele\":\"-\",\"gene\":\"CEBPA\",\"sampleCount\":1,\"studies\":[{\"histology\":\"haematopoietic neoplasm\",\"primarySite\":\"haematopoietic and lymphoid tissue\"}]}");
}
public void CosmicAlleleSpecificIndel()
{
JsonUtilities.AlleleContains("chr3 10188320 . G A . . .", Resources.MiniSuppAnnot("chr3_10188320_10188322.nsa"),
"\"id\":\"COSM18152\",\"isAlleleSpecific\":true,\"refAllele\":\"G\",\"altAllele\":\"A\",\"gene\":\"VHL\"");
}
