diff --git a/src/main/java/org/broadinstitute/hellbender/engine/ContextShard.java b/src/main/java/org/broadinstitute/hellbender/engine/ContextShard.java
deleted file mode 100644
index 25973c59200..00000000000
--- a/src/main/java/org/broadinstitute/hellbender/engine/ContextShard.java
+++ /dev/null
@@ -1,92 +0,0 @@
-package org.broadinstitute.hellbender.engine;
-
-import htsjdk.samtools.util.Locatable;
-import htsjdk.samtools.util.OverlapDetector;
-import org.broadinstitute.hellbender.utils.SimpleInterval;
-import org.broadinstitute.hellbender.utils.read.GATKRead;
-import org.broadinstitute.hellbender.utils.variant.GATKVariant;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
-import java.util.stream.Collectors;
-
-/**
- * Immutable storage class.
- * This class enforces no consistency guarantees. The intent
- * is for the reads to start in the interval and for ReadContext to have
- * all the variants and reference bases that overlap those reads, but that's up the callers.
- */
-public class ContextShard implements Serializable {
-    private static final long serialVersionUID = 1L;
-
-    // the interval covered by this shard
-    public final SimpleInterval interval;
-    // variants that overlap with the shard.
-    public final OverlapDetector<GATKVariant> variants;
-    // reads that start in the shard
-    public final List<GATKRead> reads;
-    // variants and reference for the particular read at the same index as this element.
-    public final List<ReadContextData> readContext;
-
-    public ContextShard(SimpleInterval interval) {
-        this.interval = interval;
-        this.variants = null;
-        this.reads = new ArrayList<>();
-        this.readContext = new ArrayList<>();
-    }
-
-    /**
-     * Careful: this ctor takes ownership of the passed reads and ReadContextData array.
-     * Do not modify them after this call (ideally don't even keep a reference to them).
-     */
-    private ContextShard(SimpleInterval interval, OverlapDetector<GATKVariant> variants, final List<GATKRead> reads, final List<ReadContextData> readContext) {
-        this.interval = interval;
-        this.variants = variants;
-        this.reads = reads;
-        this.readContext = readContext;
-    }
-
-    /**
-     * create a new shard, keeping only the variants that overlap
-     * with the new interval. Reads, readContext, and the variants in readContext are unchanged.
-     */
-    public ContextShard split(SimpleInterval newInterval) {
-        final OverlapDetector<GATKVariant> newVariants = variants == null ? null :
-                OverlapDetector.create( new ArrayList<>(variants.getOverlaps(newInterval)) );
-        return new ContextShard(newInterval, newVariants, reads, readContext);
-    }
-
-    /**
-     * creates a new shard, adding the specified variants.
-     * Note that readContext is unchanged (including the variants it may refer to).
-     */
-    public ContextShard withVariants(List<GATKVariant> newVariants) {
-        return new ContextShard(this.interval, OverlapDetector.create(newVariants), reads, readContext);
-    }
-
-    /**
-     * creates a new shard, adding the specified reads.
-     * Careful: this call takes ownership of the passed read array. So you can't modify it after this call.
-     */
-    public ContextShard withReads(List<GATKRead> newReads) {
-        return new ContextShard(this.interval, this.variants, newReads, readContext);
-    }
-
-    /**
-     * creates a new shard, adding the specified read context and *removing the variants*.
-     * Careful: this call takes ownership of the passed ReadContextData array. So you can't modify it after this call.
-     */
-    public ContextShard withReadContext(List<ReadContextData> newReadContext) {
-        return new ContextShard(interval, null, reads, newReadContext);
-    }
-
-    /**
-     * Returns the variants that overlap the query interval, in start-position order.
-     */
-    public List<GATKVariant> variantsOverlapping(Locatable interval) {
-        return variants.getOverlaps(interval).stream().sorted(Comparator.comparingInt(GATKVariant::getStart)).collect(Collectors.toList());
-    }
-
-}