From 7615a42777e3cf9528882a1134a14f562144d861 Mon Sep 17 00:00:00 2001 From: Andrew Chen Date: Tue, 19 Jan 2016 17:44:30 -0800 Subject: [PATCH] Changed fisher strand bias from sb to FS --- .../adam/converters/VariantAnnotationConverter.scala | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantAnnotationConverter.scala b/adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantAnnotationConverter.scala index 861bf2c7c6..28de3d5af8 100644 --- a/adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantAnnotationConverter.scala +++ b/adam-core/src/main/scala/org/bdgenomics/adam/converters/VariantAnnotationConverter.scala @@ -83,13 +83,13 @@ object VariantAnnotationConverter extends Serializable { ) val INFO_KEYS: Seq[AttrKey] = Seq( - AttrKey("fisherStrandBiasPValue", attrAsFloat _, VCFStandardHeaderLines.getInfoLine(VCFConstants.STRAND_BIAS_KEY)), AttrKey("rmsMapQ", attrAsFloat _, VCFStandardHeaderLines.getInfoLine(VCFConstants.RMS_MAPPING_QUALITY_KEY)), AttrKey("mapq0Reads", attrAsInt _, VCFStandardHeaderLines.getInfoLine(VCFConstants.MAPPING_QUALITY_ZERO_KEY)), AttrKey("mqRankSum", attrAsFloat _, new VCFInfoHeaderLine("MQRankSum", 1, VCFHeaderLineType.Float, "Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities")), AttrKey("readPositionRankSum", attrAsFloat _, new VCFInfoHeaderLine("ReadPosRankSum", 1, VCFHeaderLineType.Float, "Z-score from Wilcoxon rank sum test of Alt vs. Ref read position bias")), AttrKey("vqslod", attrAsFloat _, new VCFInfoHeaderLine("VQSLOD", 1, VCFHeaderLineType.Float, "Log odds ratio of being a true variant versus being false under the trained gaussian mixture model")), - AttrKey("culprit", attrAsString _, new VCFInfoHeaderLine("culprit", 1, VCFHeaderLineType.String, "The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out")) + AttrKey("culprit", attrAsString _, new VCFInfoHeaderLine("culprit", 1, VCFHeaderLineType.String, "The annotation which was the worst performing in the Gaussian mixture model, likely the reason why the variant was filtered out")), + AttrKey("fisherStrandBiasPValue", attrAsFloat _, new VCFInfoHeaderLine("FS", 1, VCFHeaderLineType.Float, "Phred-scaled p-value using Fisher's exact test to detect strand bias")) ) val FORMAT_KEYS: Seq[AttrKey] = Seq(