public void IntergenicVariant() { var sa = new SupplementaryAnnotationPosition(47960) { IsRefMinorAllele = true, GlobalMajorAllele = "A", GlobalMajorAlleleFrequency = "0.9239" }; var saReader = new MockSupplementaryAnnotationReader(sa); var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENST00000518655_chr1_Ensembl84"), saReader, "chr1 47960 . T . 1242.00 PASS SNVSB=-87.0;SNVHPOL=3"); Assert.NotNull(annotatedVariant); Assert.Contains("\"isReferenceMinorAllele\":true", annotatedVariant.ToString()); var altAllele = annotatedVariant.AnnotatedAlternateAlleles.FirstOrDefault(); Assert.NotNull(altAllele); // intergenic variant are not exposed in the JSON file AssertUtilities.CheckEnsemblTranscriptCount(0, altAllele); AssertUtilities.CheckRefSeqTranscriptCount(0, altAllele); }
public void DuplicatedTranscripts() { var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENST00000483270_chr1_Ensembl84"), "1 15910881 MantaBND:17185:0:1:0:9:0:0 G [2:86827867[G . MinSomaticScore SVTYPE=BND;MATEID=MantaBND:17185:0:1:0:9:0:1;CIPOS=0,7;HOMLEN=7;HOMSEQ=TGATCCG;SOMATIC;SOMATICSCORE=19;BND_DEPTH=26;MATE_BND_DEPTH=21 PR:SR 30,0:20,0 64,2:173,8"); Assert.NotNull(annotatedVariant); AssertUtilities.CheckAlleleCount(1, annotatedVariant); var altAllele = annotatedVariant.AnnotatedAlternateAlleles.First(); AssertUtilities.CheckEnsemblTranscriptCount(1, altAllele); }
public void UnwantedTranscriptInsertion() { var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("chr2_216305895_T_TAA_Ensembl84_pos"), "chr2\t216305895\t.\tT\tTAA\t130.00\tPASS\t."); Assert.NotNull(annotatedVariant); var altAllele = annotatedVariant.AnnotatedAlternateAlleles.FirstOrDefault(); Assert.NotNull(altAllele); AssertUtilities.CheckEnsemblTranscriptCount(1, altAllele); }
public void FuzzyInsertion() { var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh38("ENST00000471857_chr2_Ensembl84"), null, "chr2\t90221381\tMantaINS:49750:2:2:0:6:0\tC\t<INS>\t282\tPASS\tEND=90221390;SVTYPE=INS;LEFT_SVINSSEQ=CCGTGGCCACTCAGTTTTAGCGTCTCTGCTCTATTTGGACATTTTGCAGTTCT;RIGHT_SVINSSEQ=GATGTTGCAACTTATTACGGTCAACGGACTTACAATGCCCCTGA;DQ=0\tGT:FT:GQ:PL:PR:SR\t0/1:PASS:107:157,0,975:1,0:19,7\t0/1:PASS:175:225,0,730:1,0:14,7\t0/0:PASS:112:0,62,899:1,0:14,0"); Assert.NotNull(annotatedVariant); AssertUtilities.CheckAlleleCount(1, annotatedVariant); var altAllele = annotatedVariant.AnnotatedAlternateAlleles.First(); Assert.NotNull(altAllele); AssertUtilities.CheckEnsemblTranscriptCount(1, altAllele); }
public void NoConsequences() { var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("chr1_115256529_G_TAA_RefSeq84_pos"), "chr1 115256529 . T . . PASS . GT:GQX:DP:DPF 0/0:99:34:2"); Assert.NotNull(annotatedVariant); Assert.DoesNotContain("\"isReferenceMinorAllele\":true", annotatedVariant.ToString()); var altAllele = annotatedVariant.AnnotatedAlternateAlleles.FirstOrDefault(); Assert.NotNull(altAllele); // intergenic variant are not exposed in the JSON file AssertUtilities.CheckEnsemblTranscriptCount(0, altAllele); AssertUtilities.CheckRefSeqTranscriptCount(0, altAllele); }
public void DisableMitochondrialAnnotation() { var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENST00000387314_chrM_Ensembl84"), null, "MT 589 . C A . PASS . . ."); Assert.NotNull(annotatedVariant); AssertUtilities.CheckAlleleCount(1, annotatedVariant); var altAllele = annotatedVariant.AnnotatedAlternateAlleles.First(); Assert.NotNull(altAllele); AssertUtilities.CheckEnsemblTranscriptCount(0, altAllele); Assert.DoesNotContain("ENST00000387314", altAllele.ToString()); }
public void TranscriptInsertion5000() { var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("chr1_51801236_A_AA_Ensembl84_pos"), "chr1\t51801235\t.\tCA\tCAA,C\t134.00\tPASS\t."); Assert.NotNull(annotatedVariant); var altAllele = annotatedVariant.AnnotatedAlternateAlleles.ElementAt(0); Assert.NotNull(altAllele); AssertUtilities.CheckEnsemblTranscriptCount(7, altAllele); altAllele = annotatedVariant.AnnotatedAlternateAlleles.ElementAt(1); Assert.NotNull(altAllele); AssertUtilities.CheckEnsemblTranscriptCount(8, altAllele); }
public void UpstreamGeneVariant() { var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENST00000576171_chr17_Ensembl84"), Resources.MiniSuppAnnot("chr17_46107_46108.nsa"), "17 46107 . A . 153 LowGQX SNVSB=-20.1;SNVHPOL=4;GMAF=G|0.9988;RefMinor;CSQT=A||ENST00000576171|upstream_gene_variant GT:GQ:GQX:DP:DPF:AD 1/1:18:18:7:0:0,7"); Assert.NotNull(annotatedVariant); var altAllele = annotatedVariant.AnnotatedAlternateAlleles.First(); Assert.NotNull(altAllele); AssertUtilities.CheckEnsemblTranscriptCount(1, altAllele); var transcript = altAllele.EnsemblTranscripts.FirstOrDefault(); Assert.NotNull(transcript); // ReSharper disable once AssignNullToNotNullAttribute Assert.Equal("upstream_gene_variant", string.Join("&", transcript.Consequence)); }
public void RepeatExpansionNoConsequence() { var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENST00000601841_chrX_Ensembl84"), "chrX 146993568 FMR1 G <REPEAT:EXPANSION> 1.0 NoSuppReads REPEAT_COUNT1=30,33"); Assert.NotNull(annotatedVariant); var altAllele = annotatedVariant.AnnotatedAlternateAlleles.First(); Assert.NotNull(altAllele); AssertUtilities.CheckEnsemblTranscriptCount(1, altAllele); var transcript = altAllele.EnsemblTranscripts.FirstOrDefault(); Assert.NotNull(transcript); // ReSharper disable once PossibleNullReferenceException var observedConsequence = string.Join("&", transcript.Consequence); const string expectedConsequence = "upstream_gene_variant"; Assert.Equal(expectedConsequence, observedConsequence); }
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); }