public void BlankRefName()
{
const string vcfLine = "1 1 . N . . LowGQX END=10004;BLOCKAVG_min30p3a GT:GQX:DP:DPF .:.:0:0";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
Assert.True(variant.IsReference);
}
public void GenotypeParsing()
{
const string vcfLine = "chr1 24538137 . C . . PASS . GT:GQX:DP:DPF 0/0:99:34:2";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
Assert.True(variant.IsReference);
}
public void Insertion()
{
const string vcfLine = "chr22 15883626 P1_MEI_4726 T <INS> 40 . SVTYPE=INS;CIPOS=-23,23;IMPRECISE;NOVEL;SVMETHOD=SR;NSF5=1;NSF3=0";
var altAllele = new VariantAlternateAllele(15883627, 15883626, "T", "insertion")
{
VepVariantType = VariantType.insertion,
IsStructuralVariant = true,
AlternateAllele = "insertion"
};
var expectedReferenceName = "chr22";
var expectedAlternateAlleles = new List <VariantAlternateAllele> {
altAllele
};
var expectedVcfReferenceBegin = altAllele.Start - 1;
var expectedVcfReferenceEnd = altAllele.End;
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
Assert.Equal(expectedReferenceName, variant.ReferenceName);
Assert.Equal(expectedVcfReferenceBegin, variant.VcfReferenceBegin);
Assert.Equal(expectedVcfReferenceEnd, variant.VcfReferenceEnd);
Assert.True(expectedAlternateAlleles.SequenceEqual(variant.AlternateAlleles));
}
public void Cnv()
{
const string vcfLine = "chr1 713044 DUP_gs_CNV_1_713044_755966 C <CN0>,<CN2> 100 PASS AC=3,206;AF=0.000599042,0.0411342;AN=5008;CS=DUP_gs;END=755966;NS=2504;SVTYPE=CNV;DP=20698;EAS_AF=0.001,0.0615;AMR_AF=0.0014,0.0259;AFR_AF=0,0.0303;EUR_AF=0.001,0.0417;SAS_AF=0,0.045";
var altAllele = new VariantAlternateAllele(713045, 755966, "C", "CN0")
{
VepVariantType = VariantType.copy_number_variation,
IsStructuralVariant = true
};
var altAllele2 = new VariantAlternateAllele(713045, 755966, "C", "CN2")
{
VepVariantType = VariantType.copy_number_variation,
IsStructuralVariant = true
};
var expectedReferenceName = "chr1";
var expectedAlternateAlleles = new List <VariantAlternateAllele> {
altAllele, altAllele2
};
var expectedVcfReferenceBegin = altAllele.Start - 1;
var expectedVcfReferenceEnd = altAllele.End;
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
Assert.Equal(expectedReferenceName, variant.ReferenceName);
Assert.Equal(expectedVcfReferenceBegin, variant.VcfReferenceBegin);
Assert.Equal(expectedVcfReferenceEnd, variant.VcfReferenceEnd);
Assert.True(expectedAlternateAlleles.SequenceEqual(variant.AlternateAlleles));
}
public void Duplication2()
{
const string vcfLine = "chrX 66764988 . G <DUP> 100 PASS IMPRECISE;SVTYPE=DUP;END=66943683;SVLEN=178696;CIPOS=-1,1;CIEND=-1,1;DP=2635";
var altAllele = new VariantAlternateAllele(66764989, 66943683, "G", "duplication")
{
VepVariantType = VariantType.duplication,
IsStructuralVariant = true,
AlternateAllele = "duplication"
};
var expectedReferenceName = "chrX";
var expectedAlternateAlleles = new List <VariantAlternateAllele> {
altAllele
};
var expectedVcfReferenceBegin = altAllele.Start - 1;
var expectedVcfReferenceEnd = altAllele.End;
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
Assert.Equal(expectedReferenceName, variant.ReferenceName);
Assert.Equal(expectedVcfReferenceBegin, variant.VcfReferenceBegin);
Assert.Equal(expectedVcfReferenceEnd, variant.VcfReferenceEnd);
Assert.True(expectedAlternateAlleles.SequenceEqual(variant.AlternateAlleles));
}
public void SvBeginPosition()
{
const string vcfLine = "1 964001 . A <DEL> 79 PASS END=964423;SVTYPE=DEL;SVLEN=-422;IMPRECISE;CIPOS=-170,170;CIEND=-175,175;CSQT=1|AGRN|ENST00000379370| GT:GQ:PR 0/1:79:34,23";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
Assert.Equal(964002, variant.AlternateAlleles[0].Start);
}
public void StripUnwantedVcfInfoFields()
{
const string vcfLine = "chr4 55141055 rs1873778 A G 1000 PASS SNVSB=-9.6;SNVHPOL=3;RefMinor;AA=G;GMAF=G|0.9577;AF1000G=0.957668;EVS=0.9589|89|6503;phyloP=-5.707;cosmic=COSM1430082;CSQT=1|PDGFRA|ENST00000257290|synonymous_variant;CSQR=1|ENSR00001241308|regulatory_region_variant GT 0/1";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
Assert.Equal("SNVSB=-9.6;SNVHPOL=3", variant.VcfColumns[VcfCommon.InfoIndex]);
}
public void RepeatExpansion()
{
const string vcfLine = "chrX 146993568 FMR1 G <REPEAT:EXPANSION> 1.0 NoSuppReads REPEAT_COUNT1=30,33";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
const int expectedReferenceBegin = 146993569;
Assert.Equal(expectedReferenceBegin, variant.AlternateAlleles[0].Start);
}
public void MissingVid()
{
const string vcfLine = "chr4 92647305 MantaBND:1703:0:1:0:0:0:0 A A[JTFH01000254.1:1952[ 49 MinGQ SVTYPE=BND;MATEID=MantaBND:1703:0:1:0:0:0:1;CIPOS=0,2;HOMLEN=2;HOMSEQ=AG;BND_DEPTH=6;MATE_BND_DEPTH=3 GT:FT:GQ:PL:PR:SR 0/0:MinGQ:7:44,0,18:1,0:0,1 0/0:MinGQ:12:39,0,45:1,2:1,0 1/1:MinGQ:5:99,6,0:0,0:0,2";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
Assert.Equal("4:92647305:+:JTFH01000254.1:1952:+", variant.AlternateAlleles[0].VariantId);
}
public void BreakendVid2()
{
// NIR-941
const string vcfLine = "chr1 9121449 MantaBND:542:0:2:0:0:0:0 C [chr14:93712486[C 518 PASS SVTYPE=BND;MATEID=MantaBND:542:0:2:0:0:0:1;CIPOS=0,4;HOMLEN=4;HOMSEQ=CCTG;BND_DEPTH=49;MATE_BND_DEPTH=48 GT:GQ:PR:SR 0/1:518:33,2:32,15";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
// the naming convention for breakends is different
Assert.Equal("1:9121449:-:14:93712486:+", variant.AlternateAlleles[0].VariantId);
}
public void SvVidChrName()
{
// NIR-941
const string vcfLine = "chr1 814866 Canvas:GAIN:chr1:814867:824517 N <CNV> 4 q10;CLT10kb SVTYPE=CNV;END=824517;CSQ=CNV|upstream_gene_variant|MODIFIER|FAM41C|284593|Transcript|NR_027055.1|misc_RNA|||||||||||2685|-1|||YES|||rseq_mrna_match&rseq_ens_no_match||||||| RC:BC:CN\t214:7:4";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
// the naming convention for breakends is different
Assert.Equal("1:814867:824517:4", variant.AlternateAlleles[0].VariantId);
}
public void CanvasCopyNumberShouldNotReportInPosition()
{
const string vcfLine =
"1 723707 Canvas:GAIN:1:723708:2581225 N <CNV> 41 PASS SVTYPE=CNV;END=2581225 RC:BC:CN:MCC . 129:3123:3:2";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
Assert.Null(variant.CopyNumber);
}
public void VariantFeatureEquals(string vcfLine, bool isEqual)
{
var variant1 = VcfUtilities.GetVariant("chr4 55141055 rs1873778 A G,T 1000 PASS . .", _renamer);
var variant2 = VcfUtilities.GetVariant(vcfLine, _renamer);
Assert.Equal(isEqual, variant1.Equals(variant2));
Assert.Equal(true, variant1.Equals(variant1));
Assert.Equal(false, variant1.Equals(null));
}
public void BreakendVid1()
{
// NIR-941
const string vcfLine = "chr1 797265 MantaBND:10:0:1:0:2:0:0 G G]chr8:245687] 55 PASS SVTYPE=BND;MATEID=MantaBND:10:0:1:0:2:0:1;CIPOS=0,31;HOMLEN=31;HOMSEQ=ATTGATAGATGATAGGTAGATAGTAGATAGA;BND_DEPTH=59;MATE_BND_DEPTH=41 GT:GQ:PR:SR 0/1:55:39,6:20,3";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
// the naming convention for breakends is different
Assert.Equal("1:797265:+:8:245687:-", variant.AlternateAlleles[0].VariantId);
}
public void BreakEndBegin()
{
// NIR-1234
const string vcfLine = "1 28722335 MantaBND:4051:0:2:0:0:0:0 T [3:115024109[T . PASS SVTYPE=BND;MATEID=MantaBND:4051:0:2:0:0:0:1;IMPRECISE;CIPOS=-209,210;SOMATIC;SOMATICSCORE=42;BND_DEPTH=23;MATE_BND_DEPTH=24 PR 25,0 71,10";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
Assert.True(variant.IsStructuralVariant);
Assert.Equal(28722335, variant.AlternateAlleles[0].Start);
}
public void ParseStrandBias()
{
// NIR-1235
const string vcfLine =
"chrX 2699246 rs148553620 C A 250.95 VQSRTrancheSNP99.00to99.90 AC=2;AF=0.250;AN=8;BaseQRankSum=1.719;DB;DP=106;Dels=0.00;FS=20.202;HaplotypeScore=0.0000;MLEAC=2;MLEAF=0.250;MQ=43.50;MQ0=52;MQRankSum=2.955;QD=4.73;ReadPosRankSum=1.024;SB=-1.368e+02;VQSLOD=-0.3503;culprit=MQ;PLF GT:AD:DP:GQ:PL:AA 0:10,6:16:9:0,9,118:P1,. 0|1:12,11:23:27:115,0,27:M1,M2 0|0:37,0:37:18:0,18,236:M1,P1 1|0:13,17:30:59:177,0,59:M2,P1";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
Assert.Equal(-136.8, variant.StrandBias);
}
public void SingleNucleotideVariant()
{
var variant = VcfUtilities.GetVariant("4 100 . T A . . .", _renamer);
var altAllele = variant.AlternateAlleles[0];
const string expectedVid = "4:100:A";
var observedVid = _vid.Create(_renamer, variant.ReferenceName, altAllele);
Assert.Equal(expectedVid, observedVid);
}
public void InsertionDeletion()
{
var variant = VcfUtilities.GetVariant("4 99 . GTAGGT GCCCCCC . . .", _renamer);
const string expectedVid = "4:100:104:CCCCCC";
var altAllele = variant.AlternateAlleles[0];
var observedVid = _vid.Create(_renamer, variant.ReferenceName, altAllele);
Assert.Equal(expectedVid, observedVid);
}
public void ParseStrelkaJointSomaticNormalQuality()
{
const string vcfLine =
"9\t46530\t.\tC\tCG\t.\tQSI_ref\tSOMATIC;QSI=2;TQSI=1;NT=het;QSI_NT=2;TQSI_NT=1;SGT=ref->ref;RU=G;RC=0;IC=1;IHP=2\tDP:DP2:TAR:TIR:TOR:DP50:FDP50:SUBDP50\t13:13:10,12:3,7:0,2:14.49:0.00:0.00\t72:72:67,67:0,1:5,6:75.31:0.38:0.00";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
Assert.NotNull(variant.JointSomaticNormalQuality);
Assert.Equal(2, variant.JointSomaticNormalQuality.Value);
}
public void ParseSvLen()
{
const string vcfLine = "1 1594584 MantaDEL:164:0:1:1:0:0 C <DEL> . MGE10kb END=1660503;SVTYPE=DEL;SVLEN=-65919;IMPRECISE;CIPOS=-285,285;CIEND=-205,205;SOMATIC;SOMATICSCORE=36;ColocalizedCanvas PR 42,0 226,9";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
Assert.Equal(1594584, variant.VcfReferenceBegin);
Assert.Equal(1594585, variant.AlternateAlleles[0].Start);
Assert.Equal(1660503, variant.AlternateAlleles[0].End);
Assert.Equal(65919, variant.SvLength);
}
public void Alu()
{
const string vcfLine = "1 645710 ALU_umary_ALU_2 A <INS:ME:ALU> 100 PASS AC=35;AF=0.00698882;AN=5008;CS=ALU_umary;MEINFO=AluYa4_5,1,223,-;NS=2504;SVLEN=222;SVTYPE=ALU;TSD=null;DP=12290;EAS_AF=0.0069;AMR_AF=0.0072;AFR_AF=0;EUR_AF=0.0189;SAS_AF=0.0041";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
const string expectedVid = "1:645711:645932:MEI";
var observedVid = _vid.Create(_renamer, variant.ReferenceName, variant.AlternateAlleles[0]);
Assert.Equal(expectedVid, observedVid);
}
public void CopyNumberVariation()
{
const string vcfLine = "1 9319324 Canvas:GAIN:1:9319325:9404899 N <CNV> 36 PASS SVTYPE=CNV;END=9404899 RC:BC:CN:MCC . 144:104:6:4";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
const string expectedVid = "1:9319325:9404899:6";
var observedVid = _vid.Create(_renamer, variant.ReferenceName, variant.AlternateAlleles[0]);
Assert.Equal(expectedVid, observedVid);
}
public void CopyNumberFromSomatic()
{
// NIR-811
const string vcfLine = "1 816119 . N <CNV> 6 q10 SVTYPE=CNV;END=826343;CSQT=1|AL645608.2|ENST00000594233| RC:BC:CN 186:11:4";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
const string expectedVid = "1:816120:826343:4";
var observedVid = _vid.Create(_renamer, variant.ReferenceName, variant.AlternateAlleles[0]);
Assert.Equal(expectedVid, observedVid);
}
public void Sva()
{
const string vcfLine = "1 1517860 SVA_umary_SVA_1 A <INS:ME:SVA> 100 PASS AC=3;AF=0.000599042;AN=5008;CS=SVA_umary;MEINFO=SVA,44,394,+;NS=2504;SVLEN=350;SVTYPE=SVA;TSD=null;DP=18602;EAS_AF=0.001;AMR_AF=0;AFR_AF=0.0015;EUR_AF=0;SAS_AF=0";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
const string expectedVid = "1:1517861:1518210:MEI";
var observedVid = _vid.Create(_renamer, variant.ReferenceName, variant.AlternateAlleles[0]);
Assert.Equal(expectedVid, observedVid);
}
public void SvDeletion()
{
const string vcfLine = "1 207981229 MantaDEL:9144:0:1:0:0:0 A <DEL> . MGE10kb END=208014817;SVTYPE=DEL;SVLEN=-33588;CIPOS=0,4;CIEND=0,4;HOMLEN=4;HOMSEQ=GAGG;SOMATIC;SOMATICSCORE=44;ColocalizedCanvas PR:SR 13,0:16,0 23,4:19,4";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
const string expectedVid = "1:207981230:208014817";
var observedVid = _vid.Create(_renamer, variant.ReferenceName, variant.AlternateAlleles[0]);
Assert.Equal(expectedVid, observedVid);
}
public void SvDuplication()
{
const string vcfLine = "1 55024355 DUP_delly_DUP22372 C <CN2> 100 PASS AC=3;AF=0.000599042;AN=5008;CIEND=-150,150;CIPOS=-150,150;CS=DUP_delly;END=55050323;NS=2504;SVLEN=25968;SVTYPE=DUP;IMPRECISE;DP=19622;EAS_AF=0.001;AMR_AF=0;AFR_AF=0;EUR_AF=0;SAS_AF=0.002";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
const string expectedVid = "1:55024356:55050323:DUP";
var observedVid = _vid.Create(_renamer, variant.ReferenceName, variant.AlternateAlleles[0]);
Assert.Equal(expectedVid, observedVid);
}
public void SvInsertion()
{
const string vcfLine = "12 129771777 MantaINS:104437:0:0:0:3:0 A <INS> . PASS END=129771779;SVTYPE=INS;LEFT_SVINSSEQ=TCTCACTCATAGGTGGGAATTGAACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCT;RIGHT_SVINSSEQ=AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA;SOMATIC;SOMATICSCORE=34 PR:SR 7,0:8,0 5,0:14,9";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
const string expectedVid = "12:129771778:129771779:INS";
var observedVid = _vid.Create(_renamer, variant.ReferenceName, variant.AlternateAlleles[0]);
Assert.Equal(expectedVid, observedVid);
}
public void SvTranslocationBreakEnd()
{
const string vcfLine = "1 160359958 MantaBND:6887:0:1:0:0:0:1 G G]3:19392235] . PASS SVTYPE=BND;MATEID=MantaBND:6887:0:1:0:0:0:0;IMPRECISE;CIPOS=-137,137;SOMATIC;SOMATICSCORE=41;BND_DEPTH=22;MATE_BND_DEPTH=11 PR 21,0 41,7";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
const string expectedVid = "1:160359958:+:3:19392235:-";
var observedVid = _vid.Create(_renamer, variant.ReferenceName, variant.AlternateAlleles[0]);
Assert.Equal(expectedVid, observedVid);
}
public void SvTandemDuplication()
{
const string vcfLine = "1 224646603 MantaDUP:TANDEM:9996:0:1:0:0:0 A <DUP:TANDEM> . MGE10kb END=224800119;SVTYPE=DUP;SVLEN=153516;SVINSLEN=37;SVINSSEQ=CAAAACTTACTATAGCAGTTCTGTGAGCTGCTCTAGC;SOMATIC;SOMATICSCORE=58;ColocalizedCanvas PR:SR 26,0:20,0 51,10:60,12";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
const string expectedVid = "1:224646604:224800119:TDUP";
var observedVid = _vid.Create(_renamer, variant.ReferenceName, variant.AlternateAlleles[0]);
Assert.Equal(expectedVid, observedVid);
}
public void SvInversion()
{
const string vcfLine = "2 70850318 MantaINV:15204:1:2:0:0:0 T <INV> . MinSomaticScore END=71389878;SVTYPE=INV;SVLEN=539560;IMPRECISE;CIPOS=-134,135;CIEND=-144,145;INV5;SOMATIC;SOMATICSCORE=11 PR 9,0 31,5";
var variant = VcfUtilities.GetVariant(vcfLine, _renamer);
const string expectedVid = "2:70850319:71389878:Inverse";
var observedVid = _vid.Create(_renamer, variant.ReferenceName, variant.AlternateAlleles[0]);
Assert.Equal(expectedVid, observedVid);
}