public void GatkGenomeVcf()
{
const bool isGatkGenomeVcf = true;
var vcfVariant = VcfUtilities.GetVcfVariant("1 10360 . C <NON_REF> . PASS END=10362 GT:DP:GQ:MIN_DP:PL 0/0:198:99:196:0,120,1800", isGatkGenomeVcf);
var annotatedVariant = DataUtilities.GetVariant(Resources.CacheGRCh37("ENST00000483270_chr1_Ensembl84"), vcfVariant);
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckAlleleCount(0, annotatedVariant);
}
public void MissingRefBlockEntry()
{
const string vcfLine = "1 10005 . C . . LowGQX END=10034;BLOCKAVG_min30p3a GT:GQX:DP:DPF 0/0:3:1:0";
var vcfVariant = VcfUtilities.GetVcfVariant(vcfLine);
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, vcfLine);
var vcf = new VcfConversion();
var observedVcfLine = vcf.Convert(vcfVariant, annotatedVariant);
Assert.Equal(vcfLine, observedVcfLine);
}
public void AlleleMissingPhylop()
{
const string vcfLine = "1 4004037 . CG CA,TG 0 LowDP;LowGQ DP=0 GT:GQ:AD:VF:NL:SB:GQX ./.:0:0:0.000:20:-100.0000:0";
var vcfVariant = VcfUtilities.GetVcfVariant(vcfLine);
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, vcfLine);
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckAlleleCount(2, annotatedVariant);
var altAllele = annotatedVariant.AnnotatedAlternateAlleles.First();
DataUtilities.SetConservationScore(altAllele, "-0.344");
var vcf = new VcfConversion();
var observedVcfLine = vcf.Convert(vcfVariant, annotatedVariant);
Assert.Contains("phyloP=-0.344,.", observedVcfLine);
}
public void MixedAlleleRefMinor()
{
var vcfLine = "1 7965489 . C . . PASS RefMinor;phyloP=0.178 GT:GQX:DP:DPF 0/0:180:61:2";
var vcfVariant = VcfUtilities.GetVcfVariant(vcfLine);
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, Resources.MiniSuppAnnot("chr1_7965489_7965490.nsa"), vcfLine);
Assert.NotNull(annotatedVariant);
var altAllele = annotatedVariant.AnnotatedAlternateAlleles.First();
Assert.NotNull(altAllele);
DataUtilities.SetConservationScore(altAllele, "0.178");
var vcf = new VcfConversion();
var observedInfoField = vcf.Convert(vcfVariant, annotatedVariant).Split('\t')[VcfCommon.InfoIndex];
Assert.Equal("phyloP=0.178", observedInfoField);
}
public void AlleleSpecificPhylop()
{
const string vcfLine = "1 4004037 . CG CA,TG 0 LowDP;LowGQ DP=0 GT:GQ:AD:VF:NL:SB:GQX ./.:0:0:0.000:20:-100.0000:0";
var vcfVariant = VcfUtilities.GetVcfVariant(vcfLine);
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, vcfLine);
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckAlleleCount(2, annotatedVariant);
var altAllele = annotatedVariant.AnnotatedAlternateAlleles.ElementAt(0);
DataUtilities.SetConservationScore(altAllele, "-0.344");
var altAllele2 = annotatedVariant.AnnotatedAlternateAlleles.ElementAt(1);
DataUtilities.SetConservationScore(altAllele2, "0.135");
var vcf = new VcfConversion();
var observedVcfLine = vcf.Convert(vcfVariant, annotatedVariant).Split('\t')[VcfCommon.InfoIndex];
Assert.Contains("phyloP=-0.344,0.135", observedVcfLine);
}
public void NoPhylopScores()
{
const string vcfLine = "1 103188976 rs35710136 CTCTA ATATA,CTCTC 41 PASS SNVSB=0.0;SNVHPOL=3;AA=.,a;GMAF=A|0.09465,A|0.4898;AF1000G=.,0.510184;phyloP=-0.094 GT:GQ:GQX:DP:DPF:AD 1/2:63:16:12:1:0,7,5";
var vcfVariant = VcfUtilities.GetVcfVariant(vcfLine);
var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, vcfLine);
Assert.NotNull(annotatedVariant);
AssertUtilities.CheckAlleleCount(2, annotatedVariant);
var altAllele = annotatedVariant.AnnotatedAlternateAlleles.First();
DataUtilities.SetConservationScore(altAllele, null);
var altAllele2 = annotatedVariant.AnnotatedAlternateAlleles.ElementAt(1);
DataUtilities.SetConservationScore(altAllele2, null);
var vcf = new VcfConversion();
var observedVcfLine = vcf.Convert(vcfVariant, annotatedVariant).Split('\t')[VcfCommon.InfoIndex];
Assert.DoesNotContain("phyloP", observedVcfLine);
}
