diff --git a/src/sv-pipeline/scripts/vcf_qc/collectQC.perSample_benchmarking.sh b/src/sv-pipeline/scripts/vcf_qc/collectQC.perSample_benchmarking.sh
index a2fc5b5d6..b4f77028c 100755
--- a/src/sv-pipeline/scripts/vcf_qc/collectQC.perSample_benchmarking.sh
+++ b/src/sv-pipeline/scripts/vcf_qc/collectQC.perSample_benchmarking.sh
@@ -155,7 +155,7 @@ while read ID; do
   if [ ! -z ${VIDlist} ] && [ -s ${VIDlist} ]; then
     echo $ID
     zcat ${VCFSTATS} | head -n1 > ${OVRTMP}/SET1_calls/${ID}.SET1.SV_calls.bed
-    zcat ${VIDlist} | cut -f1 | fgrep -wf - <( zcat ${VCFSTATS} ) >> ${OVRTMP}/SET1_calls/${ID}.SET1.SV_calls.bed
+    zcat ${VIDlist} | awk '$2 != "./." {print $1}' | fgrep -wf - <( zcat ${VCFSTATS} ) >> ${OVRTMP}/SET1_calls/${ID}.SET1.SV_calls.bed
     bgzip -f ${OVRTMP}/SET1_calls/${ID}.SET1.SV_calls.bed
     rm -f ${OVRTMP}/SET1_calls/${ID}.SET1.SV_calls.bed
     tabix -f ${OVRTMP}/SET1_calls/${ID}.SET1.SV_calls.bed.gz
diff --git a/wdl/CollectQcPerSample.wdl b/wdl/CollectQcPerSample.wdl
index 2ebd232e7..200bf67aa 100644
--- a/wdl/CollectQcPerSample.wdl
+++ b/wdl/CollectQcPerSample.wdl
@@ -102,14 +102,14 @@ task CollectVidsPerSample {
       | bcftools view -i 'SVTYPE=="CNV" || AC>0' \
       | bcftools query -f '[%SAMPLE\t%ID\t%ALT\t%GT\t%GQ\t%CN\t%CNQ\n]' \
       | awk '{OFS="\t"; gt = $4; gq = $5; if ($3 == "<CNV>") { gq = $7; if ($6 == 2) { gt = "0/0" } else if ($6 == 1 || $6 == 3) { gt = "0/1" } else { gt = "1/1"} }; print $1, $2, gt, gq}' \
-      | awk -v outprefix="~{outdirprefix}" '$3 != "0/0" && $3 != "./." {OFS="\t"; print $2, $3, $4 >> outprefix"/"$1".VIDs_genotypes.txt" }'
+      | awk -v outprefix="~{outdirprefix}" '$3 != "0/0" {OFS="\t"; print $2, $3, $4 >> outprefix"/"$1".VIDs_genotypes.txt" }'
     else
       bcftools view -S ~{samples_list} ~{vcf} \
       | bcftools +fill-tags -- -t AC \
       | bcftools view -i 'SVTYPE=="CNV" || AC>0' \
       | bcftools query -f '[%SAMPLE\t%ID\t%ALT\t%GT\t%GQ\n]' \
       | awk '{OFS="\t"; gt = $4; gq = $5; if ($3 ~ /CN0/) { if ($4 == "0/2") { gt = "0/0" } else if ($4 == "0/1" || $4 == "0/3") { gt = "0/1" } else { gt = "1/1"} }; print $1, $2, gt, gq}' \
-      | awk -v outprefix="~{outdirprefix}" '$3 != "0/0" && $3 != "./." {OFS="\t"; print $2, $3, $4 >> outprefix"/"$1".VIDs_genotypes.txt" }'
+      | awk -v outprefix="~{outdirprefix}" '$3 != "0/0" {OFS="\t"; print $2, $3, $4 >> outprefix"/"$1".VIDs_genotypes.txt" }'
     fi
 
     # Gzip all output lists
diff --git a/wdl/MainVcfQc.wdl b/wdl/MainVcfQc.wdl
index bc662cfae..c5060f55f 100644
--- a/wdl/MainVcfQc.wdl
+++ b/wdl/MainVcfQc.wdl
@@ -512,12 +512,14 @@ task PlotQcPerSample {
     # Make per-sample directory
     mkdir ~{prefix}_perSample/
 
-    # Untar per-sample VID lists
+    # Untar per-sample VID lists and exclude null genotypes
     mkdir tmp_untar/
     tar -xvzf ~{per_sample_tarball} \
       --directory tmp_untar/
     find tmp_untar/ -name "*.VIDs_genotypes.txt.gz" | while read FILE; do
-      mv $FILE ~{prefix}_perSample/
+      bname=$(basename $FILE)
+      zcat $FILE | awk '$2 != "./."' | gzip -f > ~{prefix}_perSample/$bname
+      rm $FILE
     done
 
     # Plot per-sample distributions