public void SpuriousRefMinor2()
{
var saReader = ResourceUtilities.GetSupplementaryAnnotationReader(Resources.MiniSuppAnnot("chrX_1619046_1619046.nsa"));
VcfUtilities.FieldEquals(saReader,
"X 1619046 . C . . LowGQX RefMinor GT:GQX:DP:DPF 0/0:8:38:12", ".", VcfCommon.InfoIndex);
}
public void SpuriousRefMinor()
{
var saReader = ResourceUtilities.GetSupplementaryAnnotationReader(Resources.MiniSuppAnnot("chr2_190634103_190634104.nsa"));
VcfUtilities.FieldEquals(saReader, "2 190634103 . C . . HighDPFRatio .", ".",
VcfCommon.InfoIndex);
}
public void MultiDbSnpOutput()
{
var saReader = ResourceUtilities.GetSupplementaryAnnotationReader(Resources.MiniSuppAnnot("chr17_186913_186914.nsa"));
VcfUtilities.FieldEquals(saReader,
"17 186913 rs34543275,rs11453667 A AT 111 LowGQX CIGAR=1M1I;RU=T;REFREP=11;IDREP=12;GMAF=AC|0.002995;AF1000G=0.748003;CSQT=1|RPH3AL|ENST00000331302|intron_variant&feature_elongation,1||ENST00000575743|downstream_gene_variant GT:GQ:GQX:DPI:AD 1/1:21:18:9:0,7",
"rs11453667;rs34543275", VcfCommon.IdIndex);
}
public void MissingEvsValue()
{
var saReader = ResourceUtilities.GetSupplementaryAnnotationReader(Resources.MiniSuppAnnot("chr1_226259211_226259213.nsa"));
VcfUtilities.FieldEquals(saReader,
"1 226259211 rs375001380;rs397983063 TCA TA,TC 32 LowGQXHetAltDel CIGAR=1M1D1M,2M1D;RU=C,A;REFREP=1,17;IDREP=0,16;EVS=|6|5096;CSQT=1|H3F3A|ENST00000366813|3_prime_UTR_variant&feature_truncation,2|H3F3A|ENST00000366813|3_prime_UTR_variant&feature_truncation GT:GQ:GQX:DPI:AD 1/2:162:2:22:4,8,1",
"CIGAR=1M1D1M,2M1D;RU=C,A;REFREP=1,17;IDREP=0,16", VcfCommon.InfoIndex);
}
public void NotPotentialRefMinor()
{
var saReader = ResourceUtilities.GetSupplementaryAnnotationReader(Resources.MiniSuppAnnot("chr17_77263_77265.nsa"));
VcfUtilities.FieldEquals(saReader,
"17 77264 . G . 428 PASS END=77265;CIGAR=1M1D;RU=G;REFREP=4;IDREP=3 GT:GQ:GQX:DPI:AD 1/1:33:30:12:0,11",
"END=77265;CIGAR=1M1D;RU=G;REFREP=4;IDREP=3", VcfCommon.InfoIndex);
}
public void DuplicateOneKgFreq()
{
var saReader = ResourceUtilities.GetSupplementaryAnnotationReader(Resources.MiniSuppAnnot("chr5_29786207_29786208.nsa"));
VcfUtilities.FieldEquals(saReader,
"5 29786207 rs150619197 C . . SiteConflict;LowGQX END=29786207;BLOCKAVG_min30p3a;AF1000G=.,0.994409;GMAF=A|0.9944;RefMinor GT:GQX:DP:DPF 0:24:9:0",
"END=29786207;BLOCKAVG_min30p3a;RefMinor;GMAF=C|0.005591", VcfCommon.InfoIndex);
}
public void MissingRefMinorAnnotation()
{
var saReader = ResourceUtilities.GetSupplementaryAnnotationReader(Resources.MiniSuppAnnot("chr2_193187632_193187633.nsa"));
VcfUtilities.FieldEquals(saReader,
"2 193187632 . G . . LowGQX;HighDPFRatio . GT:GQX:DP:DPF .:.:0:2", "RefMinor;GMAF=G|0.01937",
VcfCommon.InfoIndex);
}
public void VariantSiteRefMinor()
{
var saReader = ResourceUtilities.GetSupplementaryAnnotationReader(Resources.MiniSuppAnnot("chr1_789256_789257.nsa"));
VcfUtilities.FieldEquals(saReader,
"1 789256 rs3131939 T C . LowGQX . GT:GQX:DP:DPF:AD 0:.:0:0:0", "GMAF=T|0.005192;AF1000G=0.994808",
VcfCommon.InfoIndex);
}
public void RefSiteRefMinor()
{
var saReader = ResourceUtilities.GetSupplementaryAnnotationReader(Resources.MiniSuppAnnot("chr1_789256_789257.nsa"));
VcfUtilities.FieldEquals(saReader,
"1 789256 rs3131939 T . . LowGQX END=789256 GT:GQX:DP:DPF:AD 0:.:0:0:0",
"END=789256;RefMinor;GMAF=T|0.005192", VcfCommon.InfoIndex);
}
public void MissingEvsDot()
{
var saReader = ResourceUtilities.GetSupplementaryAnnotationReader(Resources.MiniSuppAnnot("chr1_116609125_116609128.nsa"));
VcfUtilities.FieldEquals(saReader,
"1 116609125 rs548438731;rs3833541 CTC CC,CT 531 PASS CIGAR=1M1D1M,2M1D;RU=T,C;REFREP=1,4;IDREP=0,3;AA=T,.;GMAF=C|0.03674,.;AF1000G=0.0367412,.;EVS=0.624324|44|5731;CSQT=1|SLC22A15|ENST00000369503|intron_variant&feature_truncation,2|SLC22A15|ENST00000369503|intron_variant&feature_truncation GT:GQ:GQX:DPI:AD 1/2:574:9:58:0,13,26",
"CIGAR=1M1D1M,2M1D;RU=T,C;REFREP=1,4;IDREP=0,3;AA=T,.;AF1000G=0.036741,.;EVS=.,0.624324|44|5731",
VcfCommon.InfoIndex);
}
public void Missing1KgValues()
{
var saReader = ResourceUtilities.GetSupplementaryAnnotationReader(Resources.MiniSuppAnnot("chr17_505249_505250.nsa"));
VcfUtilities.FieldEquals(saReader,
"17 505249 . T C 35 PASS SNVSB=0.7;SNVHPOL=5 GT:GQ:GQX:DP:DPF:AD 0/1:34:31:5:1:1,4",
"SNVSB=0.7;SNVHPOL=5;GMAF=C|0.13;AF1000G=0.129992;cosmic=1|COSN16302644,1|COSN6658016",
VcfCommon.InfoIndex);
}
public void BlankInfoField()
{
VcfUtilities.FieldEquals(null,
"chr1 24538137 . C . . PASS . GT:GQX:DP:DPF 0/0:99:34:2", ".", VcfCommon.InfoIndex);
}