diff --git a/CHANGELOG.md b/CHANGELOG.md
index 361e0d8..122d731 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,10 @@
 # Changes
 
+## 1.8.2
+
+*  Update bcftools from 1.5 to version 1.9
+*  Update consolidate_vcf.pl to new standard of bcftools version 1.9
+
 ## 1.8.1
 
 * Re-structured repository to use a `Makefile.PL` for handling installation/dependency checking. For integration with Bioconda.
diff --git a/README.md b/README.md
index 15a42c8..9d244c8 100644
--- a/README.md
+++ b/README.md
@@ -31,7 +31,7 @@ conda install snvphyl-tools
 
 
 ### 2. Install dependencies using install_deps.sh
-Script will download and compile in the current working directory [bcftools](http://www.htslib.org/),[htslib](http://www.htslib.org/), [Mummer](http://mummer.sourceforge.net/) and [Vcftools](https://vcftools.github.io/index.html).
+Script will download and compile in the current working directory [bcftools](http://www.htslib.org/),[htslib](http://www.htslib.org/), [Mummer](http://mummer.sourceforge.net/) and [Vcftools](https://vcftools.github.io/index.html). Note that [samtools](http://www.htslib.org/) version 1.9 needs to be available on the PATH and will not be installed by install_deps.sh .
 
 
 #### Step a: Install Dependencies
@@ -45,11 +45,16 @@ cd snvphyl-tools
 ./install_deps.sh
 #wait patiently to completion and setup the following environment variables
 #example below
-export PATH=/home/test/snvphyl-tools/bcftools-1.5:/home/test/snvphyl-tools/MUMmer3.23:$PATH
-export BCFTOOLS_PLUGINS=/home/test//snvphyl-tools/bcftools-1.5/plugins
-PERL5LIB=/home/test/snvphyl-tools/lib/perl5
+export PATH=/home/test/snvphyl-tools/bcftools-1.9:/home/test/snvphyl-tools/MUMmer3.23:$PATH
+export BCFTOOLS_PLUGINS=/home/test//snvphyl-tools/bcftools-1.9/plugins
+export PERL5LIB=/home/test/snvphyl-tools/lib/perl5
+
+#Install samtools 1.9
+#if conda available, use command below, else build with source or apt/yum
+#conda install samtools samtools==1.9
 ```
 
+
 #### Step b: Run Tests
 -----------------
 
diff --git a/bin/consolidate_vcfs.pl b/bin/consolidate_vcfs.pl
index 81569c2..0d1f27d 100755
--- a/bin/consolidate_vcfs.pl
+++ b/bin/consolidate_vcfs.pl
@@ -65,10 +65,10 @@ sub combine_vcfs{
     #if we are using vcf files, need to convert first to vcf before applying the filter. The reason is bug with bcftools where SOME files will put the wrong FLAG in....
     if ( $ext eq '.vcf.gz')
     {
-        $cmd = "$bcftools view $mpileup -O v | $bcftools  filter -s 'coverage' -i 'DP>=$coverage_cutoff || DP4[0]+DP4[1]>=$coverage_cutoff'  $out_type > $dir/coverage_mpileup$ext";
+        $cmd = "$bcftools view $mpileup -O v | $bcftools  filter -s 'coverage' -i 'INFO/DP>=$coverage_cutoff || INFO/DP4[0]+INFO/DP4[1]>=$coverage_cutoff'  $out_type > $dir/coverage_mpileup$ext";
     }
     else {
-        $cmd = "$bcftools  filter -s 'coverage' -i 'DP>=$coverage_cutoff || DP4[0]+DP4[1]>=$coverage_cutoff' $mpileup $out_type > $dir/coverage_mpileup$ext";
+        $cmd = "$bcftools  filter -s 'coverage' -i 'INFO/DP>=$coverage_cutoff || INFO/DP4[0]+INFO/DP4[1]>=$coverage_cutoff' $mpileup $out_type > $dir/coverage_mpileup$ext";
     }
 
     system($cmd) == 0 or die "Could not run $cmd";
@@ -127,7 +127,7 @@ sub combine_vcfs{
     #if either of them fail, it will be hard clip out.
     #NB that not sure how it handles when have multiple different alternative alleles
     #also hard clipping ones that fail filtering. Do not want to have them appear in the snvalign-positions since they never passed
-    $cmd = "$bcftools  filter  -m + -e  'MQM<$min_mean_mapping || AO/DP<$ao'  $dir/0002$ext $out_type   > $dir/1-0002$ext && bcftools index $dir/1-0002$ext";
+    $cmd = "$bcftools  filter  -m + -e  'MQM<$min_mean_mapping || INFO/AO/INFO/DP<$ao'  $dir/0002$ext $out_type   > $dir/1-0002$ext && bcftools index $dir/1-0002$ext";
     system($cmd) == 0 or die "Could not run $cmd";
 
 
diff --git a/install_deps.sh b/install_deps.sh
index 9f54124..df2ce3a 100755
--- a/install_deps.sh
+++ b/install_deps.sh
@@ -14,7 +14,7 @@ DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 echo "Fetching and installing htslib...";
 
 #installing all dependencies for building bcftools and our plugin
-htslib='htslib-1.5'
+htslib='htslib-1.9'
 
 if [ ! -d "$htslib" ]; then
 
@@ -22,7 +22,7 @@ if [ ! -d "$htslib" ]; then
 fi
 
 
-curl -s https://codeload.github.com/samtools/htslib/tar.gz/1.5 > htslib.tar.gz
+curl -s https://codeload.github.com/samtools/htslib/tar.gz/1.9 > htslib.tar.gz
 tar -zxf htslib.tar.gz
 #clean up
 rm htslib.tar.gz
@@ -39,7 +39,7 @@ echo "Done!"
 
 echo "Fetching and install bcftools"
 
-bcftools='bcftools-1.5'
+bcftools='bcftools-1.9'
 
 if [ ! -d "$bcftools" ]; then
 
@@ -48,7 +48,7 @@ fi
 
 
 
-curl -s https://codeload.github.com/samtools/bcftools/tar.gz/1.5 > bcftools.tar.gz
+curl -s https://codeload.github.com/samtools/bcftools/tar.gz/1.9 > bcftools.tar.gz
 tar -zxf bcftools.tar.gz
 
 #clean up
diff --git a/t/consolidate_vcfs_input/4/output/v1.bcf.gz b/t/consolidate_vcfs_input/4/output/v1.bcf.gz
index 5f79fc7..5c7a761 100644
Binary files a/t/consolidate_vcfs_input/4/output/v1.bcf.gz and b/t/consolidate_vcfs_input/4/output/v1.bcf.gz differ
diff --git a/t/tree/expected/5/phylogeneticTree.txt b/t/tree/expected/5/phylogeneticTree.txt
old mode 100755
new mode 100644
index 437205d..7fe5f5b
--- a/t/tree/expected/5/phylogeneticTree.txt
+++ b/t/tree/expected/5/phylogeneticTree.txt
@@ -1 +1 @@
-(VC-10:0.000000,VC-1:0.000000,(C6706:1.284387,(3554-08:0.000000,(VC-19:0.000000,(VC-6:0.000000,(2011EL-2317:0.000000,((2010EL-1796:0.000000,2010EL-1786-c1_2000_2400kb:0.075801):0.000003,((VC-18:0.000000,VC-15:0.000000):0.036948,((VC-26:0.000000,(VC-25:0.000000,VC-14:0.000000):0.000000):0.036826,(2010EL-1798:0.000000,(2012V-1001:0.038164,2010EL-1749:0.038164):0.038285):0.000003):0.000003):0.000003):0.000002):0.036659):0.000003):0.000004):0.023159):0.092602);
\ No newline at end of file
+(VC-1:0.000000,VC-10:0.000000,(C6706:1.284387,(3554-08:0.000000,(VC-19:0.000000,(VC-6:0.000000,(2011EL-2317:0.000000,((2010EL-1786-c1_2000_2400kb:0.075801,2010EL-1796:0.000000):0.000003,((VC-15:0.000000,VC-18:0.000000):0.036948,((VC-26:0.000000,(VC-14:0.000000,VC-25:0.000000):0.000000):0.036826,(2010EL-1798:0.000000,(2010EL-1749:0.038164,2012V-1001:0.038164):0.038285):0.000003):0.000003):0.000003):0.000002):0.036659):0.000003):0.000004):0.023159):0.092602);
\ No newline at end of file
diff --git a/t/tree/expected/5/revisedMatrix.csv b/t/tree/expected/5/revisedMatrix.csv
old mode 100755
new mode 100644
index 6d0bad9..6d5ea1d
--- a/t/tree/expected/5/revisedMatrix.csv
+++ b/t/tree/expected/5/revisedMatrix.csv
@@ -1,18 +1,18 @@
-strain	VC-10	VC-1	C6706	3554-08	VC-19	VC-6	2011EL-2317	2010EL-1796	2010EL-1786-c1_2000_2400kb	VC-18	VC-15	VC-26	VC-25	VC-14	2010EL-1798	2012V-1001	2010EL-1749	
-VC-10	0	0	19	3	3	3	4	4	6	5	5	5	5	5	4	6	6	
-VC-1	0	0	19	3	3	3	4	4	6	5	5	5	5	5	4	6	6	
-C6706	19	19	0	18	18	18	19	19	21	20	20	20	20	20	19	21	21	
-3554-08	3	3	18	0	0	0	1	1	3	2	2	2	2	2	1	3	3	
-VC-19	3	3	18	0	0	0	1	1	3	2	2	2	2	2	1	3	3	
-VC-6	3	3	18	0	0	0	1	1	3	2	2	2	2	2	1	3	3	
-2011EL-2317	4	4	19	1	1	1	0	0	2	1	1	1	1	1	0	2	2	
-2010EL-1796	4	4	19	1	1	1	0	0	2	1	1	1	1	1	0	2	2	
-2010EL-1786-c1_2000_2400kb	6	6	21	3	3	3	2	2	0	3	3	3	3	3	2	4	4	
-VC-18	5	5	20	2	2	2	1	1	3	0	0	2	2	2	1	3	3	
-VC-15	5	5	20	2	2	2	1	1	3	0	0	2	2	2	1	3	3	
-VC-26	5	5	20	2	2	2	1	1	3	2	2	0	0	0	1	3	3	
-VC-25	5	5	20	2	2	2	1	1	3	2	2	0	0	0	1	3	3	
-VC-14	5	5	20	2	2	2	1	1	3	2	2	0	0	0	1	3	3	
-2010EL-1798	4	4	19	1	1	1	0	0	2	1	1	1	1	1	0	2	2	
-2012V-1001	6	6	21	3	3	3	2	2	4	3	3	3	3	3	2	0	2	
-2010EL-1749	6	6	21	3	3	3	2	2	4	3	3	3	3	3	2	2	0	
+strain	VC-1	VC-10	C6706	3554-08	VC-19	VC-6	2011EL-2317	2010EL-1786-c1_2000_2400kb	2010EL-1796	VC-15	VC-18	VC-26	VC-14	VC-25	2010EL-1798	2010EL-1749	2012V-1001	
+VC-1	0	0	19	3	3	3	4	6	4	5	5	5	5	5	4	6	6	
+VC-10	0	0	19	3	3	3	4	6	4	5	5	5	5	5	4	6	6	
+C6706	19	19	0	18	18	18	19	21	19	20	20	20	20	20	19	21	21	
+3554-08	3	3	18	0	0	0	1	3	1	2	2	2	2	2	1	3	3	
+VC-19	3	3	18	0	0	0	1	3	1	2	2	2	2	2	1	3	3	
+VC-6	3	3	18	0	0	0	1	3	1	2	2	2	2	2	1	3	3	
+2011EL-2317	4	4	19	1	1	1	0	2	0	1	1	1	1	1	0	2	2	
+2010EL-1786-c1_2000_2400kb	6	6	21	3	3	3	2	0	2	3	3	3	3	3	2	4	4	
+2010EL-1796	4	4	19	1	1	1	0	2	0	1	1	1	1	1	0	2	2	
+VC-15	5	5	20	2	2	2	1	3	1	0	0	2	2	2	1	3	3	
+VC-18	5	5	20	2	2	2	1	3	1	0	0	2	2	2	1	3	3	
+VC-26	5	5	20	2	2	2	1	3	1	2	2	0	0	0	1	3	3	
+VC-14	5	5	20	2	2	2	1	3	1	2	2	0	0	0	1	3	3	
+VC-25	5	5	20	2	2	2	1	3	1	2	2	0	0	0	1	3	3	
+2010EL-1798	4	4	19	1	1	1	0	2	0	1	1	1	1	1	0	2	2	
+2010EL-1749	6	6	21	3	3	3	2	4	2	3	3	3	3	3	2	0	2	
+2012V-1001	6	6	21	3	3	3	2	4	2	3	3	3	3	3	2	2	0