diff --git a/scripts/align_reference.sh b/scripts/align_reference.sh
index b45556b..1612bb3 100644
--- a/scripts/align_reference.sh
+++ b/scripts/align_reference.sh
@@ -87,12 +87,12 @@ for i in "${LARRAY[@]}"; do
 	if [ ! -f $DIR/01_mapped/$SAMPLENAME\_$LANE.mapped.sam ]; then
 		bwa mem -M -t $NUM_CORES $REF_GENOME $FASTQ/$SAMPLENAME\_$LANE\_R1_001.fastq.gz \
 		$FASTQ/$SAMPLENAME\_$LANE\_R2_001.fastq.gz > $DIR/01_mapped/$SAMPLENAME\_$LANE.mapped.sam
-		touch check_tmp_align/.$SAMPLENAME\_$LANE_map_sam_check
-	elif [ ! -e check_tmp_align/.$SAMPLENAME\_$LANE_map_sam_check ]; then
+		touch check_tmp_align/.$SAMPLENAME\_$LANE_\map_sam_check
+	elif [ ! -e check_tmp_align/.$SAMPLENAME\_$LANE\_map_sam_check ]; then
 		rm $DIR/01_mapped/$SAMPLENAME\_$LANE.mapped.sam
 		bwa mem -M -t $NUM_CORES $REF_GENOME $FASTQ/$SAMPLENAME\_$LANE\_R1_001.fastq.gz \
 		$FASTQ/$SAMPLENAME\_$LANE\_R2_001.fastq.gz > $DIR/01_mapped/$SAMPLENAME\_$LANE.mapped.sam
-		touch check_tmp_align/.$SAMPLENAME\_$LANE_map_sam_check
+		touch check_tmp_align/.$SAMPLENAME\_$LANE\_map_sam_check
 	fi
 
 	# convert SAM to BAM and fix read pairing information and flags
@@ -100,12 +100,12 @@ for i in "${LARRAY[@]}"; do
 	if [ ! -f $DIR/01_mapped/$SAMPLENAME\_$LANE.mapped.bam ]; then
 		samtools fixmate -O bam $DIR/01_mapped/$SAMPLENAME\_$LANE.mapped.sam \
 		$DIR/01_mapped/$SAMPLENAME\_$LANE.mapped.bam
-		touch check_tmp_align/.$SAMPLENAME\_$LANE_sam_bam
-	elif [ ! -e check_tmp_align/.$SAMPLENAME\_$LANE_sam_bam ]; then
+		touch check_tmp_align/.$SAMPLENAME\_$LANE\_sam_bam
+	elif [ ! -e check_tmp_align/.$SAMPLENAME\_$LANE\_sam_bam ]; then
 		rm $DIR/01_mapped/$SAMPLENAME\_$LANE.mapped.bam
 		samtools fixmate -O bam $DIR/01_mapped/$SAMPLENAME\_$LANE.mapped.sam \
 		$DIR/01_mapped/$SAMPLENAME\_$LANE.mapped.bam
-		touch check_tmp_align/.$SAMPLENAME\_$LANE_sam_bam
+		touch check_tmp_align/.$SAMPLENAME\_$LANE\_sam_bam
 	fi
 
 
@@ -114,13 +114,13 @@ for i in "${LARRAY[@]}"; do
 		samtools sort -T $DIR/01_mapped/$SAMPLENAME\_$LANE.mapped -O bam -@ $NUM_CORES \
 		-o $DIR/01_mapped/$SAMPLENAME\_$LANE.mapped.sorted.bam \
 		$DIR/01_mapped/$SAMPLENAME\_$LANE.mapped.bam
-		touch check_tmp_align/.$SAMPLENAME\_$LANE_sort_bam
-	elif [ ! -e check_tmp_align/.$SAMPLENAME\_$LANE_sort_bam ]; then
+		touch check_tmp_align/.$SAMPLENAME\_$LANE\_sort_bam
+	elif [ ! -e check_tmp_align/.$SAMPLENAME\_$LANE\_sort_bam ]; then
 		rm $DIR/01_mapped/$SAMPLENAME\_$LANE.mapped.sorted.bam
 		samtools sort -T $DIR/01_mapped/$SAMPLENAME\_$LANE.mapped -O bam -@ $NUM_CORES \
 		-o $DIR/01_mapped/$SAMPLENAME\_$LANE.mapped.sorted.bam \
 		$DIR/01_mapped/$SAMPLENAME\_$LANE.mapped.bam
-		touch check_tmp_align/.$SAMPLENAME\_$LANE_sort_bam
+		touch check_tmp_align/.$SAMPLENAME\_$LANE\_sort_bam
 	fi
 
 done
diff --git a/scripts/call_variants.sh b/scripts/call_variants.sh
index 2f2fd1c..59b59e5 100644
--- a/scripts/call_variants.sh
+++ b/scripts/call_variants.sh
@@ -75,12 +75,12 @@ fi
 
 # create bed file from bam file
 if [ ! -f $BAM_DIR/$SAMPLENAME.depth ];then
-	samtools depth -a $BAM > \
+	samtools depth -a $BAM -q 20 -Q 30 > \
 	$BAM_DIR/$SAMPLENAME.depth
 	touch check_tmp_variant/.$SAMPLENAME.bam_depth
 elif [ ! -e check_tmp_variant/.$SAMPLENAME.bam_depth ]; then
 	rm $BAM_DIR/$SAMPLENAME.depth
-	samtools depth -a $BAM > \
+	samtools depth -a $BAM -q 20 -Q 30 > \
 	$BAM_DIR/$SAMPLENAME.depth
 	touch check_tmp_variant/.$SAMPLENAME.bam_depth
 fi
@@ -132,7 +132,57 @@ elif [ ! -e check_tmp_variant/.$SAMPLENAME.vcf_bcftools_filt ]; then
 	touch check_tmp_variant/.$SAMPLENAME.vcf_bcftools_filt
 fi
 
+# mask bcftool filtered positions
+# concat bcftool filtered-masked positions with depth-masked bed file
 
+if [ ! -f $DIR/04_assembly/$SAMPLENAME.allmask.bed ]; then
+	bcftools filter --no-version -i "(INFO/AD[1])/(INFO/AD[0]+INFO/AD[1]) < $SNP_SUPPORT" \
+	$DIR/03_variants/$SAMPLENAME.bcftools.vcf -o $DIR/03_variants/$SAMPLENAME.bcftools.lowsupport.vcf
+	awk '(/^[^#]/ && length($4) == length($5)) {printf "%s\t%d\t%d\n", $1, $2 - 1, $2}' \
+	$DIR/03_variants/$SAMPLENAME.bcftools.lowsupport.vcf > $DIR/03_variants/$SAMPLENAME.lowsupport.bed
+
+	bcftools filter --no-version -i "INFO/ADF[1] < $REQ_STRAND_DEPTH || INFO/ADR[1] < $REQ_STRAND_DEPTH" \
+	$DIR/03_variants/$SAMPLENAME.bcftools.vcf -o $DIR/03_variants/$SAMPLENAME.bcftools.lowstranddepth.vcf
+	awk '(/^[^#]/ && length($4) == length($5)) {printf "%s\t%d\t%d\n", $1, $2 - 1, $2}' \
+	$DIR/03_variants/$SAMPLENAME.bcftools.lowstranddepth.vcf > $DIR/03_variants/$SAMPLENAME.lowstranddepth.bed
+
+
+	cat $DIR/03_variants/$SAMPLENAME.lowsupport.bed $DIR/03_variants/$SAMPLENAME.lowstranddepth.bed > \
+	$DIR/03_variants/$SAMPLENAME.vcffiltered.bed
+
+	cat $DIR/03_variants/$SAMPLENAME.vcffiltered.bed $DIR/04_assembly/$SAMPLENAME.depthmask.bed | \
+	uniq > $DIR/04_assembly/$SAMPLENAME.allmask.bed
+
+	touch check_tmp_variant/.$SAMPLENAME.all_mask_bed
+
+elif [ ! -e check_tmp_variant/.$SAMPLENAME.all_mask_bed ]; then
+
+	rm -f $DIR/03_variants/$SAMPLENAME.bcftools.lowsupport.vcf
+	rm -f $DIR/03_variants/$SAMPLENAME.lowsupport.bed
+	rm -f $DIR/03_variants/$SAMPLENAME.bcftools.lowstranddepth.vcf
+	rm -f $DIR/03_variants/$SAMPLENAME.lowstranddepth.bam_depth
+	rm -f $DIR/03_variants/$SAMPLENAME.vcffiltered.bed
+	rm -f $DIR/04_assembly/$SAMPLENAME.allmask.bed
+
+	bcftools filter --no-version -i "(INFO/AD[1])/(INFO/AD[0]+INFO/AD[1]) < $SNP_SUPPORT" \
+	$DIR/03_variants/$SAMPLENAME.bcftools.vcf -o $DIR/03_variants/$SAMPLENAME.bcftools.lowsupport.vcf
+	awk '(/^[^#]/ && length($4) == length($5)) {printf "%s\t%d\t%d\n", $1, $2 - 1, $2}' \
+	$DIR/03_variants/$SAMPLENAME.bcftools.lowsupport.vcf > $DIR/03_variants/$SAMPLENAME.lowsupport.bed
+
+	bcftools filter --no-version -i "INFO/ADF[1] < $REQ_STRAND_DEPTH || INFO/ADR[1] < $REQ_STRAND_DEPTH" \
+	$DIR/03_variants/$SAMPLENAME.bcftools.vcf -o $DIR/03_variants/$SAMPLENAME.bcftools.lowstranddepth.vcf
+	awk '(/^[^#]/ && length($4) == length($5)) {printf "%s\t%d\t%d\n", $1, $2 - 1, $2}' \
+	$DIR/03_variants/$SAMPLENAME.bcftools.lowstranddepth.vcf > $DIR/03_variants/$SAMPLENAME.lowstranddepth.bed
+
+
+	cat $DIR/03_variants/$SAMPLENAME.lowsupport.bed $DIR/03_variants/$SAMPLENAME.lowstranddepth.bed > \
+	$DIR/03_variants/$SAMPLENAME.vcffiltered.bed
+
+	cat $DIR/03_variants/$SAMPLENAME.vcffiltered.bed $DIR/04_assembly/$SAMPLENAME.depthmask.bed | \
+	uniq > $DIR/04_assembly/$SAMPLENAME.allmask.bed
+
+	touch check_tmp_variant/.$SAMPLENAME.all_mask_bed
+fi
 
 # left align and normalize indels
 # then remove insertions to avoid issues with multi-alignment later on