diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/MultialleleCounter.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/MultialleleCounter.java
deleted file mode 100644
index fec6a83c..00000000
--- a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/MultialleleCounter.java
+++ /dev/null
@@ -1,44 +0,0 @@
-package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype;
-
-import java.io.*;
-import java.util.ArrayList;
-import java.util.TreeSet;
-import java.util.concurrent.ConcurrentHashMap;
-
-import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMasks;
-import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantSpec;
-import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantStore;
-import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedByteIndexedStorage;
-
-public class MultialleleCounter {
-
-    public static void main(String[] args) throws ClassNotFoundException, IOException {
-        VariantStore variantStore = VariantStore.readInstance("/opt/local/hpds/all/");
-        for (String contig : variantStore.getVariantMaskStorage().keySet()) {
-            System.out.println("Starting contig : " + contig);
-            FileBackedByteIndexedStorage<Integer, ConcurrentHashMap<String, VariantMasks>>
-                    currentChromosome = variantStore.getVariantMaskStorage().get(contig);
-            currentChromosome.keys().parallelStream().forEach((offsetBucket) -> {
-                System.out.println("Starting bucket : " + offsetBucket);
-                ConcurrentHashMap<String, VariantMasks> maskMap;
-                maskMap = currentChromosome.get(offsetBucket);
-
-                TreeSet<VariantSpec> variantsSortedByOffset = new TreeSet<>();
-                for (String variant : maskMap.keySet()) {
-                    variantsSortedByOffset.add(new VariantSpec(variant));
-                }
-                ArrayList<VariantSpec> variantsSortedByOffsetList = new ArrayList<>(variantsSortedByOffset);
-                for (int y = 1; y < variantsSortedByOffsetList.size(); y++) {
-                    if (variantsSortedByOffsetList.get(y).metadata.offset.equals(variantsSortedByOffsetList.get(y - 1).metadata.offset)) {
-                        try {
-                            System.out.println("Matching offsets : " + variantsSortedByOffsetList.get(y - 1).specNotation() + " : " + variantsSortedByOffsetList.get(y).specNotation() + ":" + maskMap.get(variantsSortedByOffsetList.get(y - 1).specNotation()).heterozygousMask.toString(2) + ":" + ":" + maskMap.get(variantsSortedByOffsetList.get(y).specNotation()).heterozygousMask.toString(2));
-                        } catch (NullPointerException e) {
-                            System.out.println("Matching offsets : " + variantsSortedByOffsetList.get(y - 1).specNotation() + " : " + variantsSortedByOffsetList.get(y).specNotation());
-                        }
-                    }
-                }
-                System.out.println("Completed bucket : " + offsetBucket);
-            });
-        }
-    }
-}
diff --git a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VariantCounter.java b/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VariantCounter.java
deleted file mode 100644
index 4d22c572..00000000
--- a/etl/src/main/java/edu/harvard/hms/dbmi/avillach/hpds/etl/genotype/VariantCounter.java
+++ /dev/null
@@ -1,28 +0,0 @@
-package edu.harvard.hms.dbmi.avillach.hpds.etl.genotype;
-
-import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantMasks;
-import edu.harvard.hms.dbmi.avillach.hpds.data.genotype.VariantStore;
-import edu.harvard.hms.dbmi.avillach.hpds.storage.FileBackedByteIndexedStorage;
-
-import java.io.IOException;
-import java.util.concurrent.ConcurrentHashMap;
-
-public class VariantCounter {
-
-	public static void main(String[] args) throws ClassNotFoundException, IOException {
-		VariantStore variantStore = VariantStore.readInstance("/opt/local/hpds/all/");
-		for(String contig : variantStore.getVariantMaskStorage().keySet()) {
-			int[] countOfVariants = {0};
-			FileBackedByteIndexedStorage<Integer, ConcurrentHashMap<String, VariantMasks>>
-			currentChromosome = variantStore.getVariantMaskStorage().get(contig);
-			currentChromosome.keys().parallelStream().forEach((offsetBucket)->{
-				ConcurrentHashMap<String, VariantMasks> maskMap;
-				maskMap = currentChromosome.get(offsetBucket);
-				if(maskMap!=null) {
-					countOfVariants[0]+=maskMap.size();
-				}
-			});
-			System.out.println(contig + "," + countOfVariants[0]);
-		}
-	}
-}