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);
}