diff --git a/.github/actions/purge-runner-disk/action.yml b/.github/actions/purge-runner-disk/action.yml
index d9bd987bbe9..dc86fbd7794 100644
--- a/.github/actions/purge-runner-disk/action.yml
+++ b/.github/actions/purge-runner-disk/action.yml
@@ -7,6 +7,12 @@ runs:
#https://github.com/actions/runner-images/issues/2840
- name: Reclaim some runner disk space
run: |
+ sudo df -h
+ echo "$AGENT_TOOLSDIRECTORY"
sudo rm -rf /usr/share/dotnet
sudo rm -rf "$AGENT_TOOLSDIRECTORY"
+ sudo rm -rf /usr/local/lib/android
+ sudo rm -rf /opt/ghc
+ sudo docker image prune --all --force
+ sudo df -h
shell: bash
diff --git a/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh b/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh
index 97305996d54..50dd3bcd1f0 100644
--- a/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh
+++ b/scripts/cnv_cromwell_tests/germline/run_cnv_germline_workflows.sh
@@ -1,5 +1,5 @@
#!/bin/bash -l
-set -e
+#set -e
MODE=$1
# We split up the test into CASE in COHORT to reduce overall test runtime
@@ -42,7 +42,10 @@ echo "Running ========"
# Cohort WES w/ explicit GC correction
if [[ "$MODE" == "COHORT" ]]; then
java -jar ${CROMWELL_JAR} run $WORKING_DIR/gatk/scripts/cnv_wdl/germline/cnv_germline_cohort_workflow.wdl -i cnv_germline_cohort_workflow_mod.json ;
- find /home/runner/work/gatk/gatk/scripts/cnv_cromwell_tests/germline/cromwell-executions/CNVGermlineCohortWorkflow/ | grep 'stdout\|stderr' | xargs cat ;
+ if [[ "$?" != 0 ]]; then
+ find /home/runner/work/gatk/gatk/scripts/cnv_cromwell_tests/germline/cromwell-executions/CNVGermlineCohortWorkflow/ | grep 'stdout\|stderr' | xargs cat ;
+ exit 1 ;
+ fi
fi
# Scattered case WES w/ explicit GC correction
diff --git a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants.java b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
index 70c4c46b724..b38853e6134 100644
--- a/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
+++ b/src/main/java/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants.java
@@ -28,11 +28,11 @@
* Left-align indels in a variant callset
*
*
- * This tool takes a VCF file, left-aligns the indels and trims common bases from indels,
+ * This tool takes a VCF file, left-aligns the indels and trims common bases from all variants,
* leaving them with a minimum representation. The same indel can often be placed at multiple positions and still
* represent the same haplotype. While the standard convention with VCF is to place an indel at the left-most position
* this isn't always done, so this tool can be used to left-align them. This tool optionally splits multiallelic
- * sites into biallelics and left-aligns individual alleles. Optionally, the tool will not trim common bases from indels.
+ * sites into biallelics and left-aligns individual alleles. Optionally, the tool will not trim common bases from variants.
*
*
* Input
@@ -172,8 +172,10 @@ public class LeftAlignAndTrimVariants extends VariantWalker {
private VariantContextWriter vcfWriter = null;
private VCFHeader vcfHeader = null;
- VariantContext lastVariant;
-
+ private int thisVariantGroupStart = 0;
+ private String thisVariantGroupContig = null;
+ private VariantContext lastVariantWritten = null;
+ private final List realignedVariants = new ArrayList<>();
@Override
public void onTraversalStart() {
final Map vcfHeaders = Collections.singletonMap(getDrivingVariantsFeatureInput().getName(), getHeaderForVariants());
@@ -213,6 +215,17 @@ private Set createVCFHeaderLineList(Map vcfHea
*/
@Override
public void apply(VariantContext vc, ReadsContext readsContext, ReferenceContext ref, FeatureContext featureContext) {
+ if (vc.getContig() != thisVariantGroupContig || vc.getStart() > thisVariantGroupStart) {
+ realignedVariants.sort(Comparator.comparingInt(VariantContext::getStart));
+ for (VariantContext realignedVariant : realignedVariants) {
+ vcfWriter.add(realignedVariant);
+ }
+ thisVariantGroupStart = vc.getStart();
+ thisVariantGroupContig = vc.getContig();
+ lastVariantWritten = realignedVariants.isEmpty() ? lastVariantWritten : realignedVariants.get(realignedVariants.size() - 1);
+ realignedVariants.clear();
+ }
+
final List vcList;
if (splitMultiallelics) {
if (vc.getGenotypes().stream().anyMatch(g -> g.hasAnyAttribute(GATKVCFConstants.ALLELE_FRACTION_KEY))) {
@@ -231,12 +244,10 @@ public void apply(VariantContext vc, ReadsContext readsContext, ReferenceContext
if (indelLength > maxIndelSize) {
logger.info(String.format("%s (%d) at position %s:%d; skipping that record. Set --max-indel-length >= %d",
"Indel is too long", indelLength, splitVariant.getContig(), splitVariant.getStart(), indelLength));
- lastVariant = splitVariant;
- vcfWriter.add(splitVariant);
+ realignedVariants.add(splitVariant);
} else {
- final int distanceToLastVariant = (lastVariant != null && splitVariant.contigsMatch(lastVariant)) ? splitVariant.getStart() - lastVariant.getEnd() : Integer.MAX_VALUE;
- lastVariant = GATKVariantContextUtils.leftAlignAndTrim(splitVariant, ref, Math.min(maxLeadingBases, distanceToLastVariant - 1), !dontTrimAlleles);
- vcfWriter.add(lastVariant);
+ final int distanceToLastVariant = (lastVariantWritten != null && splitVariant.contigsMatch(lastVariantWritten)) ? splitVariant.getStart() - lastVariantWritten.getStart() : Integer.MAX_VALUE;
+ realignedVariants.add(GATKVariantContextUtils.leftAlignAndTrim(splitVariant, ref, Math.min(maxLeadingBases, distanceToLastVariant), !dontTrimAlleles));
}
}
}
@@ -256,6 +267,11 @@ public boolean requiresReference() {
*/
@Override
public Object onTraversalSuccess() {
+ //write out remaining variants
+ realignedVariants.sort(Comparator.comparingInt(VariantContext::getStart));
+ for (VariantContext realignedVariant : realignedVariants) {
+ vcfWriter.add(realignedVariant);
+ }
return "SUCCESS";
}
diff --git a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java
index 2df684087e4..6dd20811d72 100644
--- a/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java
+++ b/src/main/java/org/broadinstitute/hellbender/utils/variant/GATKVariantContextUtils.java
@@ -2220,15 +2220,13 @@ public static List removeItemsByIndex(List data, List indexes
* By definition, it will only take biallelic vc's. Splitting into multiple alleles has to be
* handled by calling routine.
*
- * @param vc Input VC with variants to left align
+ * @param vc Input VC with variants to left align and trim
* @param ref Reference context
* @return new VC.
*/
- public static VariantContext leftAlignAndTrim(final VariantContext vc, final ReferenceContext ref, final int maxLeadingBases, final boolean trim) {
- if (!vc.isIndel() || maxLeadingBases <= 0) {
- return vc;
- }
+ public static VariantContext leftAlignAndTrim(final VariantContext vc, final ReferenceContext ref, final int maxLeadingBasesIndel, final boolean trim) {
+ final int maxLeadingBases = vc.isIndel() ? maxLeadingBasesIndel : 0;
for(int leadingBases = Math.min(maxLeadingBases, 10); leadingBases <= maxLeadingBases; leadingBases = Math.min(2*leadingBases, maxLeadingBases)) {
final int refStart = Math.max(vc.getStart() - leadingBases, 1);
@@ -2245,8 +2243,9 @@ public static VariantContext leftAlignAndTrim(final VariantContext vc, final Ref
return result;
}).collect(Collectors.toList());
+ final int boundStart = vc.isSNP() || vc.isMNP() ? variantOffsetInRef : variantOffsetInRef + 1; // +1 to ignore the shared base in front for indels
final List alleleRanges = vc.getAlleles().stream()
- .map(a -> new IndexRange(variantOffsetInRef + 1, variantOffsetInRef + a.length())) // +1 to ignore the shared base in front
+ .map(a -> new IndexRange(boundStart, variantOffsetInRef + a.length()))
.collect(Collectors.toList());
// note that this also shifts the index ranges as a side effect, so below they can be used to output allele bases
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38.vcf
index 05df02709e0..d87372b77ca 100755
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38.vcf
@@ -35,5 +35,14 @@ chr21 10382389 . A ATT 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
chr21 10388233 . GGAA G 30 . AC=1;AF=0.250;AN=2 GT 0/1 ./.
chr21 10804284 . T TGC 30 . AC=1;AF=0.250;AN=2 GT 0/1 ./.
chr21 13255296 . A G 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
-chr21 13255297 . AAA A 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
+chr21 13255296 . AAA A 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
chr21 39583817 . CTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT C 30 . AC=3;AF=0.750;AN=4 GT 1/1 0/1
+chr21 39584859 . C G 30 . AC=3;AF=0.750;AN=4 GT 1/1 0/1
+chr21 39584950 . C G,CC 30 . AC=2,1;AF=0.500,0.250;AN=4 GT 1/1 0/2
+chr21 39584953 . AA AG,A 30 . AC=2,1;AF=0.500,0.250;AN=4 GT 1/1 0/2
+chr21 39586243 . TAAAA T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586243 . TA T 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39586243 . T TA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39586245 . A G 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586743 . TACC T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586744 . AC A 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize296.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize296.vcf
index ee3325842fd..20289443963 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize296.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize296.vcf
@@ -35,5 +35,14 @@ chr21 10382389 . A ATT 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
chr21 10388233 . GGAA G 30 . AC=1;AF=0.250;AN=2 GT 0/1 ./.
chr21 10804284 . T TGC 30 . AC=1;AF=0.250;AN=2 GT 0/1 ./.
chr21 13255296 . A G 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
-chr21 13255297 . AAA A 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
+chr21 13255296 . AAA A 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
chr21 39583817 . CTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT C 30 . AC=3;AF=0.750;AN=4 GT 1/1 0/1
+chr21 39584859 . C G 30 . AC=3;AF=0.750;AN=4 GT 1/1 0/1
+chr21 39584950 . C G,CC 30 . AC=2,1;AF=0.500,0.250;AN=4 GT 1/1 0/2
+chr21 39584953 . AA AG,A 30 . AC=2,1;AF=0.500,0.250;AN=4 GT 1/1 0/2
+chr21 39586243 . TAAAA T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586243 . TA T 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39586243 . T TA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39586245 . A G 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586743 . TACC T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586744 . AC A 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize342.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize342.vcf
index 107ff0811e9..4d533e66553 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize342.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_maxIndelSize342.vcf
@@ -35,5 +35,14 @@ chr21 10382389 . A ATT 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
chr21 10388233 . GGAA G 30 . AC=1;AF=0.250;AN=2 GT 0/1 ./.
chr21 10804284 . T TGC 30 . AC=1;AF=0.250;AN=2 GT 0/1 ./.
chr21 13255296 . A G 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
-chr21 13255297 . AAA A 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
+chr21 13255296 . AAA A 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
chr21 39583817 . CTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT C 30 . AC=3;AF=0.750;AN=4 GT 1/1 0/1
+chr21 39584859 . C G 30 . AC=3;AF=0.750;AN=4 GT 1/1 0/1
+chr21 39584950 . C G,CC 30 . AC=2,1;AF=0.500,0.250;AN=4 GT 1/1 0/2
+chr21 39584953 . AA AG,A 30 . AC=2,1;AF=0.500,0.250;AN=4 GT 1/1 0/2
+chr21 39586243 . TAAAA T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586243 . TA T 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39586243 . T TA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39586245 . A G 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586743 . TACC T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586744 . AC A 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim.vcf
index 3c5f0086bf6..bc3b85de197 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim.vcf
@@ -35,5 +35,14 @@ chr21 10382389 . A ATT 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
chr21 10388233 . GGAA G 30 . AC=1;AF=0.250;AN=2 GT 0/1 ./.
chr21 10804284 . T TGC 30 . AC=1;AF=0.250;AN=2 GT 0/1 ./.
chr21 13255296 . A G 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
-chr21 13255297 . AAA A 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
+chr21 13255296 . AAA A 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
chr21 39583817 . CTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT C 30 . AC=3;AF=0.750;AN=4 GT 1/1 0/1
+chr21 39584859 . CAA GAA 30 . AC=3;AF=0.750;AN=4 GT 1/1 0/1
+chr21 39584950 . C G,CC 30 . AC=2,1;AF=0.500,0.250;AN=4 GT 1/1 0/2
+chr21 39584953 . AA AG,A 30 . AC=2,1;AF=0.500,0.250;AN=4 GT 1/1 0/2
+chr21 39586239 . CAATT CAATTA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39586240 . AATTA AATT 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39586243 . TAAAA TAGAA 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586243 . TAAAA T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586743 . TACC T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586744 . AC A 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim_split_multiallelics.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim_split_multiallelics.vcf
index 80ea5bb296d..75d2f190dd8 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim_split_multiallelics.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_notrim_split_multiallelics.vcf
@@ -37,5 +37,16 @@ chr21 10382389 . A ATT 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
chr21 10388233 . GGAA G 30 . AC=1;AF=0.250;AN=2 GT 0/1 ./.
chr21 10804284 . T TGC 30 . AC=1;AF=0.250;AN=2 GT 0/1 ./.
chr21 13255296 . A G 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
-chr21 13255297 . AAA A 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
+chr21 13255296 . AAA A 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
chr21 39583817 . CTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT C 30 . AC=3;AF=0.750;AN=4 GT 1/1 0/1
+chr21 39584859 . CAA GAA 30 . AC=3;AF=0.750;AN=4 GT 1/1 0/1
+chr21 39584948 . A AC 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39584950 . C G 30 . AC=2;AF=0.500;AN=4 GT 1/1 0/0
+chr21 39584951 . CA C 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39584953 . AA AG 30 . AC=2;AF=0.500;AN=4 GT 1/1 0/0
+chr21 39586239 . CAATT CAATTA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39586240 . AATTA AATT 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39586243 . TAAAA TAGAA 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586243 . TAAAA T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586743 . TACC T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586744 . AC A 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
\ No newline at end of file
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics.vcf
index 52f63f0419b..7721f6271a1 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics.vcf
@@ -37,5 +37,16 @@ chr21 10382389 . A ATT 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
chr21 10388233 . GGAA G 30 . AC=1;AF=0.250;AN=2 GT 0/1 ./.
chr21 10804284 . T TGC 30 . AC=1;AF=0.250;AN=2 GT 0/1 ./.
chr21 13255296 . A G 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
-chr21 13255297 . AAA A 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
+chr21 13255296 . AAA A 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
chr21 39583817 . CTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT C 30 . AC=3;AF=0.750;AN=4 GT 1/1 0/1
+chr21 39584859 . C G 30 . AC=3;AF=0.750;AN=4 GT 1/1 0/1
+chr21 39584948 . A AC 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39584950 . C G 30 . AC=2;AF=0.500;AN=4 GT 1/1 0/0
+chr21 39584951 . CA C 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39584954 . A G 30 . AC=2;AF=0.500;AN=4 GT 1/1 0/0
+chr21 39586243 . TAAAA T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586243 . TA T 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39586243 . T TA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39586245 . A G 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586743 . TACC T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586744 . AC A 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
\ No newline at end of file
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics_keepOrigAC.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics_keepOrigAC.vcf
index 4007fb39696..80194bc7d8c 100644
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics_keepOrigAC.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/expected_left_align_hg38_split_multiallelics_keepOrigAC.vcf
@@ -40,5 +40,16 @@ chr21 10382389 . A ATT 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
chr21 10388233 . GGAA G 30 . AC=1;AF=0.250;AN=2 GT 0/1 ./.
chr21 10804284 . T TGC 30 . AC=1;AF=0.250;AN=2 GT 0/1 ./.
chr21 13255296 . A G 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
-chr21 13255297 . AAA A 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
+chr21 13255296 . AAA A 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
chr21 39583817 . CTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCT C 30 . AC=3;AF=0.750;AN=4 GT 1/1 0/1
+chr21 39584859 . C G 30 . AC=3;AF=0.750;AN=4 GT 1/1 0/1
+chr21 39584948 . A AC 30 . AC=1;AC_Orig=1;AF=0.250;AF_Orig=0.250;AN=4;AN_Orig=4 GT 0/0 0/1
+chr21 39584950 . C G 30 . AC=2;AC_Orig=2;AF=0.500;AF_Orig=0.500;AN=4;AN_Orig=4 GT 1/1 0/0
+chr21 39584951 . CA C 30 . AC=1;AC_Orig=1;AF=0.250;AF_Orig=0.250;AN=4;AN_Orig=4 GT 0/0 0/1
+chr21 39584954 . A G 30 . AC=2;AC_Orig=2;AF=0.500;AF_Orig=0.500;AN=4;AN_Orig=4 GT 1/1 0/0
+chr21 39586243 . TAAAA T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586243 . TA T 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39586243 . T TA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39586245 . A G 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586743 . TACC T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586744 . AC A 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
diff --git a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf
index 410fa01cd77..26690f59eaf 100755
--- a/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf
+++ b/src/test/resources/org/broadinstitute/hellbender/tools/walkers/variantutils/LeftAlignAndTrimVariants/test_left_align_hg38.vcf
@@ -37,3 +37,12 @@ chr21 10804284 . T TGC 30 . AC=1;AF=0.250;AN=2 GT 0/1 ./.
chr21 13255296 . A G 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
chr21 13255301 . AAA A 30 . AC=2;AF=0.500;AN=2 GT 1/1 ./.
chr21 39584006 . CTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCCTTCCC C 30 . AC=3;AF=0.750;AN=4 GT 1/1 0/1
+chr21 39584859 . CAA GAA 30 . AC=3;AF=0.750;AN=4 GT 1/1 0/1
+chr21 39584950 . C G,CC 30 . AC=2,1;AF=0.500,0.250;AN=4 GT 1/1 0/2
+chr21 39584953 . AA AG,A 30 . AC=2,1;AF=0.500,0.250;AN=4 GT 1/1 0/2
+chr21 39586243 . TAAAA TAGAA 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586243 . TAAAA T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586243 . TAAAA TAAA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39586243 . TAAAA TAAAAA 30 . AC=1;AF=0.250;AN=4 GT 0/0 0/1
+chr21 39586743 . TACC T 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0
+chr21 39586745 . CC C 30 . AC=1;AF=0.250;AN=4 GT 0/1 0/0