Write base quality to VCF

seppinho · Mar 3, 2024 · b465d3b · b465d3b
1 parent e08a03b
commit b465d3b
Show file tree

Hide file tree

Showing 3 changed files with 20 additions and 1 deletion.
diff --git a/src/main/java/genepi/mut/objects/Variant.java b/src/main/java/genepi/mut/objects/Variant.java
@@ -16,6 +16,7 @@ public class Variant {
 	private double minorLevel;
 	private int coverage;
 	private int type;
+	private double meanBaseQualiy;
 
 	public int getPos() {
 		return pos;
@@ -117,4 +118,12 @@ public Filter getFilter() {
 	public void setFilter(Filter filter) {
 		this.filter = filter;
 	}
+
+	public double getMeanBaseQualiy() {
+		return meanBaseQualiy;
+	}
+
+	public void setMeanBaseQualiy(double meanBaseQualiy) {
+		this.meanBaseQualiy = meanBaseQualiy;
+	}
 }
diff --git a/src/main/java/genepi/mut/pileup/VcfWriter.java b/src/main/java/genepi/mut/pileup/VcfWriter.java
@@ -155,6 +155,7 @@ public void createVCF(String in, String out, String reference, String chromosome
 						final GenotypeBuilder gb = new GenotypeBuilder(sample.getId(), Arrays.asList(varAllele));
 						gb.DP(variant.getCoverage());
 						gb.attribute("AF", variant.getLevel());
+						gb.attribute("BQ", variant.getMeanBaseQualiy());
 
 						genotypes.add(gb.make());
 
@@ -197,6 +198,7 @@ public void createVCF(String in, String out, String reference, String chromosome
 						}
 
 						gb.attribute("AF", alleleFreq);
+						gb.attribute("BQ", variant.getMeanBaseQualiy());
 
 						genotypes.add(gb.make());
 
@@ -239,6 +241,9 @@ private VCFHeader generateHeader(String chromosome, int length, String command)
 		header.addMetaDataLine(new VCFFormatHeaderLine("AF", 1, VCFHeaderLineType.String,
 				"Inferred Allele Frequency of top (non-reference) allele"));
 
+		header.addMetaDataLine(new VCFFormatHeaderLine("BQ", 1, VCFHeaderLineType.String,
+				"Mean Base Quality of ALT Allele"));
+
 		header.addMetaDataLine(new VCFFormatHeaderLine("DP", 1, VCFHeaderLineType.Integer, "Read Depth"));
 
 		return header;

diff --git a/src/main/java/genepi/mut/util/MutationServerReader.java b/src/main/java/genepi/mut/util/MutationServerReader.java
@@ -45,6 +45,7 @@ public HashMap<String, Sample> parse(double requiredHetLevel) {
 
 			double majorLevel = 0;
 			double minorLevel = 0;
+			double meanBaseQuality = 0;
 			int coverage = -1;
 			int pos;
 
@@ -72,6 +73,10 @@ public HashMap<String, Sample> parse(double requiredHetLevel) {
 			if (reader.hasColumn("Coverage")) {
 				coverage = reader.getInteger("Coverage");
 			}
+
+			if (reader.hasColumn("MeanBaseQuality")) {
+				meanBaseQuality = Double.valueOf(reader.getString("MeanBaseQuality"));
+			}
 
 			sample.setId(id);
 
@@ -88,7 +93,7 @@ public HashMap<String, Sample> parse(double requiredHetLevel) {
 			variant.setMinor(minor);
 			variant.setMajorLevel(majorLevel);
 			variant.setMinorLevel(minorLevel);
-			variant.setCoverage(coverage);
+			variant.setMeanBaseQualiy(meanBaseQuality);
 			variant.setType(type);
 
 			sample.addVariant(variant);