public void BreakEnd()
{
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, null,
"chr2 13394888 MantaBND:543:0:1:0:0:0:0 G G]chr15:20404341] 114 MaxDepth SVTYPE=BND;MATEID=MantaBND:543:0:1:0:0:0:1;CIPOS=0,3;HOMLEN=3;HOMSEQ=AGT;BND_DEPTH=10;MATE_BND_DEPTH=7 GT:FT:GQ:PL:PR:SR 0/1:PASS:83:133,0,93:2,0:1,3 0/1:PASS:30:80,0,68:3,2:0,3 0/0:MinGQ:11:40,0,153:2,0:2,1");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckJsonContains("\"altAlleles\":[\"G]chr15:20404341]\"]", annotatedVariant);
}
public void IndelVariantType()
{
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, null,
"chr1 23259022 MantaDEL:58:0:1:0:0:0 GAGGATCACTTGAGCCCAGGAGTTCCAGACCAGCCCGGGCAACATGGTGAAACCCCACCTCTACAAAAAATACAAAAGTTACCCAGGCATGGTGGCACATGCCTATAGTCCCAGCTGCTGGGAGGGTTGAGGTGGGAGGATCACTTGAGCCAGGGAGGTGGAGACTGCAGTGAGCCATGATCACACCACTGCATTCAAGCCTAGGCTGCAACCTCGAGATTTTTTTTTTTTTTGAGATCCTGTCTCAAAAAAAATTTTTTTTGGCCAGGTGCGGTGGCTCACGCCTGTAATCCCAGCACTTTGGGAGGCTGAGGCGGGC GT 95 PASS END=23259340;SVTYPE=DEL;SVLEN=-318;CIGAR=1M1I318D GT:FT:GQ:PL:PR:SR 0/0:PASS:50:0,1,2:1,0:0,0 1/1:MinGQ:7:147,9,0:0,0:1,3 0/0:PASS:53:0,3,59:0,0:1,0");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckJsonContains("\"variantType\":\"indel\"", annotatedVariant);
}
public void MantaInsertionRsId()
{
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, Resources.MiniSuppAnnotGRCh38("chr1_186774064_186774065.nsa"),
"chr1 186774064 MantaINS:338:0:0:0:0:0 C CTATATATATACTTTATATATACTGTATGTGTATATATAAAGTATATATATAGTG 101 MinGQ END=186774064;SVTYPE=INS;SVLEN=54;CIGAR=1M54I;CIPOS=0,8;HOMLEN=8;HOMSEQ=TATATATA GT:FT:GQ:PL:PR:SR 0/0:MinGQ:4:48,3,0:0,0:0,1 0/0:MinGQ:3:50,3,0:0,0:0,1 1/1:MinGQ:7:148,9,0:0,0:0,3");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckJsonContains("rs57376790", annotatedVariant);
}
public void RefNameMismatch()
{
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, Resources.MiniSuppAnnot("chr1_672000_672092.nsa"),
"chr1 672000 . C <DEL> 0.1 LowQ SVTYPE=DEL;END=672092;ALTDEDUP=1;ALTDUP=0;REFDEDUP=0;REFDUP=0;INTERGENIC=False . .");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckJsonContains("dgv1n111", annotatedVariant);
}
public void SuppIntervalCnv()
{
var annotatedVariant = DataUtilities.GetSuppIntervalVariant(Resources.MiniSuppAnnot("chr1_713035_713060.nsa"),
"chr1 713045 . T <CN1> . LowGQX;HighDPFRatio END=718045;SVTYPE=CNV;BLOCKAVG_min30p3a GT:GQX:DP:DPF .:.:0:1");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckIntervalCount(28, annotatedVariant);
AssertUtilities.CheckJsonContains("variantType\":\"copy_number_variation\"", annotatedVariant);
}
public void SvDelPartiallyOverlappingGene()
{
var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENST00000546909_chr14_Ensembl84"),
"14 19443800 . G <DEL> . PASS SVTYPE=DEL;END=19452000");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckJsonContains("\"overlappingGenes\":[\"RP11-536C10.15\"]", annotatedVariant);
AssertUtilities.CheckJsonContains("ENST00000546909", annotatedVariant);
}
public void IsTheSameAsGene()
{
var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENST00000546909_chr14_Ensembl84"),
"14 19443725 14_19443847 G <CNV> . PASS SVTYPE=CNV;END=19443847;CN=0;CNscore=13.41;LOH=0;ensembl_gene_id=ENSG00000257990,ENSG00000257558");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckJsonContains("\"overlappingGenes\":[\"RP11-536C10.15\"]", annotatedVariant);
AssertUtilities.CheckJsonDoesNotContain("ENST00000546909", annotatedVariant);
}
public void InsertionReciprocalOverlap()
{
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, Resources.MiniSuppAnnot("chr1_756265_756269.nsa"),
"1 756267 . T <INS> . PASS SVTYPE=INS;END=756267");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckJsonDoesNotContain("\"reciprocalOverlap\":NaN", annotatedVariant);
AssertUtilities.CheckJsonContains("esv1032937", annotatedVariant);
AssertUtilities.CheckJsonDoesNotContain("\"reciprocalOverlap\"", annotatedVariant);
}
public void CosmicMultiDelete()
{
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, Resources.MiniSuppAnnot("chr17_21319650_21319651.nsa"),
"17 21319650 . CGAG C 101 PASS CIGAR=1M3D;RU=GAG;REFREP=2;IDREP=1 GT:GQ:GQX:DPI:AD 0/1:141:101:29:22,4");
AssertUtilities.CheckJsonContains(
"{\"id\":\"COSM3735158\",\"refAllele\":\"G\",\"altAllele\":\"-\",\"gene\":\"KCNJ12\",\"sampleCount\":1,\"studies\":[{\"histology\":\"malignant melanoma\",\"primarySite\":\"skin\"}]}",
annotatedVariant);
AssertUtilities.CheckJsonContains(
"{\"id\":\"COSM278475\",\"isAlleleSpecific\":true,\"refAllele\":\"GAG\",\"altAllele\":\"-\",\"gene\":\"KCNJ12\",\"sampleCount\":3",
annotatedVariant);
}
public void CosmicAltAllele()
{
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, Resources.MiniSuppAnnot("chr17_6928019_6928021.nsa"),
"17 6928019 . C CCAG 209 LowGQX . GT:GQ:GQX:DPI:AD 1/1:12:9:5:0,4");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckJsonContains(
"{\"id\":\"COSM983707\",\"isAlleleSpecific\":true,\"refAllele\":\"-\",\"altAllele\":\"CAG\",\"gene\":\"BCL6B_ENST00000293805\",\"sampleCount\":27",
annotatedVariant);
AssertUtilities.CheckJsonContains(
"{\"id\":\"COSM983708\",\"isAlleleSpecific\":true,\"refAllele\":\"-\",\"altAllele\":\"CAG\",\"gene\":\"BCL6B\",\"sampleCount\":27,\"",
annotatedVariant);
}
public void CosmicAltAlleleN()
{
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, Resources.MiniSuppAnnot("chr1_17086085_17086086.nsa"),
"1 17086085 . G GC 209 LowGQX . GT:GQ:GQX:DPI:AD 1/1:12:9:5:0,4");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckJsonContains(
"{\"id\":\"COSM424569\",\"refAllele\":\"-\",\"altAllele\":\"N\",\"gene\":\"Q13209_HUMAN\",\"sampleCount\":8",
annotatedVariant);
AssertUtilities.CheckJsonContains(
"{\"id\":\"COSM424570\",\"refAllele\":\"-\",\"altAllele\":\"N\",\"gene\":\"MST1P9\",\"sampleCount\":8",
annotatedVariant);
}
public void LossOfHeterozygosityTest()
{
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, null,
"1 11131485 Canvas:REF:1:11131486:16833263 N <CNV> 61 PASS SVTYPE=LOH;END=16833263 RC:BC:CN:MCC . 84:9227:2:2");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckJsonDoesNotContain("\"variantType\":\"loss_of_heterozygosity\"", annotatedVariant);
AssertUtilities.CheckJsonContains("\"variantType\":\"copy_number_variation\"", annotatedVariant);
AssertUtilities.CheckJsonDoesNotContain("\"altAllele\":\"LOH\"", annotatedVariant);
AssertUtilities.CheckSampleCount(2, annotatedVariant);
var sample = JsonUtilities.GetSampleJson(annotatedVariant, 1);
Assert.Contains("lossOfHeterozygosity", sample);
}
public void IntronNumbers()
{
var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENST00000380060_chrX_Ensembl84"),
"chrX 17705850 rs397759640;rs5901624 C CT 1815.96 PASS . . .");
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckAlleleCount(1, annotatedVariant);
var altAllele = annotatedVariant.AnnotatedAlternateAlleles.First();
Assert.NotNull(altAllele);
AssertUtilities.CheckEnsemblTranscriptCount(1, altAllele);
var transcript = altAllele.EnsemblTranscripts.FirstOrDefault();
Assert.NotNull(transcript);
Assert.Equal("1/7", transcript.Introns);
AssertUtilities.CheckJsonContains("\"introns\":\"1/7\"", annotatedVariant);
}
