diff --git a/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/factories/VariantAggregatedVcfFactory.java b/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/factories/VariantAggregatedVcfFactory.java
index 55ffb129..ebd7da27 100644
--- a/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/factories/VariantAggregatedVcfFactory.java
+++ b/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/factories/VariantAggregatedVcfFactory.java
@@ -18,7 +18,6 @@
 
 import uk.ac.ebi.eva.commons.core.models.VariantStatistics;
 import uk.ac.ebi.eva.commons.core.models.factories.exception.IncompleteInformationException;
-import uk.ac.ebi.eva.commons.core.models.factories.exception.NonVariantException;
 import uk.ac.ebi.eva.commons.core.models.genotype.Genotype;
 import uk.ac.ebi.eva.commons.core.models.pipeline.Variant;
 import uk.ac.ebi.eva.commons.core.models.pipeline.VariantSourceEntry;
@@ -395,18 +394,23 @@ protected void addGenotypeWithGTS(Variant variant, VariantSourceEntry sourceEntr
     }
 
     @Override
-    protected void checkVariantInformation(Variant variant, String fileId, String studyId)
-            throws NonVariantException, IncompleteInformationException {
-        super.checkVariantInformation(variant, fileId, studyId);
+    protected boolean checkVariantInformation(Variant variant, String fileId, String studyId)
+            throws IncompleteInformationException {
+        if (!super.checkVariantInformation(variant, fileId, studyId)) {
+            return false;
+        }
 
         if (requireEvidence) {
             VariantSourceEntry variantSourceEntry = variant.getSourceEntry(fileId, studyId);
             if (!canAlleleFrequenciesBeCalculated(variantSourceEntry)) {
                 throw new IncompleteInformationException(variant);
             } else if (variantFrequencyIsZero(variantSourceEntry)) {
-                throw new NonVariantException("The variant " + variant + " has allele frequency or counts '0'");
+                logger.warn("The variant {} has allele frequency or counts '0' and will be discarded as a non-variant",
+                            variant);
+                return false;
             }
         }
+        return true;
     }
 
     protected boolean canAlleleFrequenciesBeCalculated(VariantSourceEntry variantSourceEntry) {
diff --git a/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/factories/VariantGenotypedVcfFactory.java b/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/factories/VariantGenotypedVcfFactory.java
index 2ecade6b..4dd2d95e 100644
--- a/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/factories/VariantGenotypedVcfFactory.java
+++ b/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/factories/VariantGenotypedVcfFactory.java
@@ -16,7 +16,6 @@
 package uk.ac.ebi.eva.commons.core.models.factories;
 
 import uk.ac.ebi.eva.commons.core.models.factories.exception.IncompleteInformationException;
-import uk.ac.ebi.eva.commons.core.models.factories.exception.NonVariantException;
 import uk.ac.ebi.eva.commons.core.models.genotype.Genotype;
 import uk.ac.ebi.eva.commons.core.models.pipeline.Variant;
 import uk.ac.ebi.eva.commons.core.models.pipeline.VariantSourceEntry;
@@ -109,13 +108,18 @@ private String processGenotypeField(int alternateAlleleIdx, String genotype) {
     }
 
     @Override
-    protected void checkVariantInformation(Variant variant, String fileId, String studyId)
-            throws NonVariantException, IncompleteInformationException {
-        super.checkVariantInformation(variant, fileId, studyId);
+    protected boolean checkVariantInformation(Variant variant, String fileId, String studyId)
+            throws IncompleteInformationException {
+        if (!super.checkVariantInformation(variant, fileId, studyId)) {
+            return false;
+        }
         VariantSourceEntry variantSourceEntry = variant.getSourceEntry(fileId, studyId);
         if (!hasAlternateAlleleCalls(variantSourceEntry)) {
-            throw new NonVariantException("The variant " + variant + " has no alternate allele genotype calls");
+            logger.warn("The variant {} has no alternate allele genotype calls and will be discarded as a non-variant",
+                        variant);
+            return false;
         }
+        return true;
     }
 
     private boolean hasAlternateAlleleCalls(VariantSourceEntry variantSourceEntry) {
diff --git a/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/factories/VariantVcfFactory.java b/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/factories/VariantVcfFactory.java
index 377a8231..238d967d 100644
--- a/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/factories/VariantVcfFactory.java
+++ b/variation-commons-core/src/main/java/uk/ac/ebi/eva/commons/core/models/factories/VariantVcfFactory.java
@@ -38,7 +38,8 @@
  * Abstract class to parse the basic fields in VCF lines
  */
 public abstract class VariantVcfFactory {
-    private final static Logger logger = LoggerFactory.getLogger(VariantVcfFactory.class);
+
+    protected final static Logger logger = LoggerFactory.getLogger(VariantVcfFactory.class);
 
     public static final String ALLELE_FREQUENCY = "AF";
 
@@ -100,16 +101,13 @@ public List<Variant> create(String fileId, String studyId, String line)
             // Fill the rest of fields (after samples because INFO depends on them)
             setOtherFields(variant, fileId, studyId, ids, quality, filter, info, altAlleleIdx, alternateAlleles, line);
 
-            try {
-                checkVariantInformation(variant, fileId, studyId);
+            if (checkVariantInformation(variant, fileId, studyId)) {
                 variants.add(variant);
-            } catch (NonVariantException nve) {
-                logger.warn("The variant {} will be discarded as it is a non-variant: {}", variant, nve);
             }
         }
 
         if (variants.isEmpty()) {
-            throw new NonVariantException("No valid variants could be found");
+            logger.warn("No valid variants could be found");
         }
 
         return variants;
@@ -312,13 +310,19 @@ protected static int mapToMultiallelicIndex(int parsedAllele, int numAllele) {
         return correctedAllele;
     }
 
-    protected void checkVariantInformation(Variant variant, String fileId, String studyId)
-            throws NonVariantException, IncompleteInformationException {
+    protected boolean checkVariantInformation(Variant variant, String fileId, String studyId)
+            throws IncompleteInformationException {
         if (variant.getAlternate().equalsIgnoreCase(variant.getReference())) {
-            throw new NonVariantException("The variant " + variant + " reference and alternate alleles are the same");
+            logger.warn(
+                    "The variant {} reference and alternate alleles are the same and will be discarded as a " +
+                            "non-variant",
+                    variant);
+            return false;
         }
         if (variant.getAlternate().equals(".")) {
-            throw new NonVariantException("The variant " + variant + " has no alternate allele");
+            logger.warn("The variant {} has no alternate allele and will be discarded as a non-variant", variant);
+            return false;
         }
+        return true;
     }
 }
diff --git a/variation-commons-core/src/test/java/uk/ac/ebi/eva/commons/core/models/factories/VariantAggregatedVcfFactoryTest.java b/variation-commons-core/src/test/java/uk/ac/ebi/eva/commons/core/models/factories/VariantAggregatedVcfFactoryTest.java
index 210b4655..96ede577 100644
--- a/variation-commons-core/src/test/java/uk/ac/ebi/eva/commons/core/models/factories/VariantAggregatedVcfFactoryTest.java
+++ b/variation-commons-core/src/test/java/uk/ac/ebi/eva/commons/core/models/factories/VariantAggregatedVcfFactoryTest.java
@@ -15,12 +15,18 @@
  */
 package uk.ac.ebi.eva.commons.core.models.factories;
 
+import ch.qos.logback.classic.Level;
+import ch.qos.logback.classic.Logger;
+import ch.qos.logback.classic.spi.ILoggingEvent;
+import ch.qos.logback.core.read.ListAppender;
+import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
+import org.slf4j.LoggerFactory;
+
 import uk.ac.ebi.eva.commons.core.models.VariantStatistics;
 import uk.ac.ebi.eva.commons.core.models.factories.exception.IncompleteInformationException;
-import uk.ac.ebi.eva.commons.core.models.factories.exception.NonVariantException;
 import uk.ac.ebi.eva.commons.core.models.genotype.Genotype;
 import uk.ac.ebi.eva.commons.core.models.pipeline.Variant;
 
@@ -46,6 +52,17 @@ public class VariantAggregatedVcfFactoryTest {
     @Rule
     public ExpectedException thrown = ExpectedException.none();
 
+    private ListAppender<ILoggingEvent> listAppender;
+
+    @Before
+    public void setUp() {
+        // Set up appender to capture log messages
+        Logger factoryLogger = (Logger) LoggerFactory.getLogger(VariantVcfFactory.class);
+        listAppender = new ListAppender<>();
+        listAppender.start();
+        factoryLogger.addAppender(listAppender);
+    }
+
     @Test
     public void parseAC_AN() {
         String line = "1\t54722\t.\tTTC\tT,TCTC\t999\tPASS\tDP4=3122,3282,891,558;DP=22582;INDEL;IS=3,0.272727;VQSLOD=6.76;AN=3854;AC=889,61;TYPE=del,ins;HWE=0;ICF=-0.155251";   // structure like uk10k
@@ -137,8 +154,8 @@ public void getGenotype() {
     public void variantWithAlleleFrequencyZero() {
         String line = "1\t10040\trs123\tT\tC\t.\t.\tAF=0";
 
-        thrown.expect(NonVariantException.class);
         factory.create(FILE_ID, STUDY_ID, line);
+        assertNonVariantLogged();
     }
 
     @Test
@@ -155,8 +172,8 @@ public void multiallelicWithAlleleFrequencyZero() {
     public void variantWithAlleleCountZero() {
         String line = "1\t10040\trs123\tT\tC\t.\t.\tAN=5;AC=0";
 
-        thrown.expect(NonVariantException.class);
         factory.create(FILE_ID, STUDY_ID, line);
+        assertNonVariantLogged();
     }
 
     @Test
@@ -173,8 +190,8 @@ public void multiAlleleWithOneAlleleCountZero() {
     public void variantWithAlleleTotalNumberZero() {
         String line = "1\t10040\trs123\tT\tC\t.\t.\tAN=0;AC=5";
 
-        thrown.expect(NonVariantException.class);
         factory.create(FILE_ID, STUDY_ID, line);
+        assertNonVariantLogged();
     }
 
     @Test
@@ -220,4 +237,10 @@ public void testMultiallelicVariantWithNoAlleleCountsOrFrequency() {
         thrown.expect(IncompleteInformationException.class);
         factory.create(FILE_ID, STUDY_ID, line);
     }
+
+    private void assertNonVariantLogged() {
+        List<ILoggingEvent> logsList = listAppender.list;
+        assertTrue(logsList.get(0).getMessage().contains("non-variant"));
+        assertEquals(Level.WARN, logsList.get(0).getLevel());
+    }
 }
diff --git a/variation-commons-core/src/test/java/uk/ac/ebi/eva/commons/core/models/factories/VariantGenotypedVcfFactoryTest.java b/variation-commons-core/src/test/java/uk/ac/ebi/eva/commons/core/models/factories/VariantGenotypedVcfFactoryTest.java
index a981c360..ba24ec4b 100644
--- a/variation-commons-core/src/test/java/uk/ac/ebi/eva/commons/core/models/factories/VariantGenotypedVcfFactoryTest.java
+++ b/variation-commons-core/src/test/java/uk/ac/ebi/eva/commons/core/models/factories/VariantGenotypedVcfFactoryTest.java
@@ -15,10 +15,16 @@
  */
 package uk.ac.ebi.eva.commons.core.models.factories;
 
+import ch.qos.logback.classic.Level;
+import ch.qos.logback.classic.Logger;
+import ch.qos.logback.classic.spi.ILoggingEvent;
+import ch.qos.logback.core.read.ListAppender;
+import org.junit.Before;
 import org.junit.Rule;
 import org.junit.Test;
 import org.junit.rules.ExpectedException;
-import uk.ac.ebi.eva.commons.core.models.factories.exception.NonVariantException;
+import org.slf4j.LoggerFactory;
+
 import uk.ac.ebi.eva.commons.core.models.pipeline.Variant;
 import uk.ac.ebi.eva.commons.core.models.pipeline.VariantSourceEntry;
 
@@ -42,6 +48,17 @@ public class VariantGenotypedVcfFactoryTest {
     @Rule
     public ExpectedException thrown = ExpectedException.none();
 
+    private ListAppender<ILoggingEvent> listAppender;
+
+    @Before
+    public void setUp() {
+        // Set up appender to capture log messages
+        Logger factoryLogger = (Logger) LoggerFactory.getLogger(VariantVcfFactory.class);
+        listAppender = new ListAppender<>();
+        listAppender.start();
+        factoryLogger.addAppender(listAppender);
+    }
+
     @Test
     public void testCreateVariant_Samples() {
         String line = "1\t10040\trs123\tT\tC\t.\t.\t.\tGT\t0/0\t0/1\t0/.\t./1\t1/1"; // 5 samples
@@ -433,40 +450,40 @@ public void testMultiallelicVariantWitnNoSampleInformation() {
     public void variantWithNoAltGenotypes() {
         String line = "1\t10040\trs123\tT\tC\t.\t.\t.\tGT\t0/0\t0|0\t./.\t0|0\t./.";
 
-        thrown.expect(NonVariantException.class);
         factory.create(FILE_ID, STUDY_ID, line);
+        assertNonVariantLogged();
     }
 
     @Test
     public void haploidVariantWithNoAltGenotypes() {
         String line = "Y\t10040\trs123\tT\tC\t.\t.\t.\tGT\t.\t0\t0\t.";
 
-        thrown.expect(NonVariantException.class);
         factory.create(FILE_ID, STUDY_ID, line);
+        assertNonVariantLogged();
     }
 
     @Test
     public void triploidVariantWithNoAltGenotypes() {
         String line = "1\t10040\trs123\tT\tC\t.\t.\t.\tGT\t0/0/0\t0|0|0\t././.\t0|0|0\t././.";
 
-        thrown.expect(NonVariantException.class);
         factory.create(FILE_ID, STUDY_ID, line);
+        assertNonVariantLogged();
     }
 
     @Test
     public void variantWhereAllGenotypesAreMissingValues() {
         String line = "1\t10040\trs123\tT\tC\t.\t.\t.\tGT\t./.\t./.\t./.\t./.\t./.";
 
-        thrown.expect(NonVariantException.class);
         factory.create(FILE_ID, STUDY_ID, line);
+        assertNonVariantLogged();
     }
 
     @Test
     public void variantWhereAllGenotypesAreReference() {
         String line = "1\t10040\trs123\tT\tC\t.\t.\t.\tGT\t0/0\t0|0\t0/0\t0|0\t0/0";
 
-        thrown.expect(NonVariantException.class);
         factory.create(FILE_ID, STUDY_ID, line);
+        assertNonVariantLogged();
     }
 
     @Test
@@ -491,4 +508,10 @@ public void infoAttributesWontBeValidated() {
         assertEquals(expResult, result);
     }
 
+    private void assertNonVariantLogged() {
+        List<ILoggingEvent> logsList = listAppender.list;
+        assertTrue(logsList.get(0).getMessage().contains("non-variant"));
+        assertEquals(Level.WARN, logsList.get(0).getLevel());
+    }
+
 }