diff --git a/BALSAMIC/assets/scripts/edit_vcf_info.py b/BALSAMIC/assets/scripts/edit_vcf_info.py
index e1769b494..c1f1609dc 100644
--- a/BALSAMIC/assets/scripts/edit_vcf_info.py
+++ b/BALSAMIC/assets/scripts/edit_vcf_info.py
@@ -44,7 +44,7 @@ def edit_vcf_info(input_vcf, output_vcf, variant_caller):
 
     new_vcf = Writer(output_vcf, vcf)
 
-    with gzip.open(output_vcf, "wb"):
+    with open(output_vcf, "wb"):
         for variant in vcf:
             variant.INFO["FOUND_IN"] = variant_caller + "|" + output_vcf
             new_vcf.write_record(variant)
diff --git a/BALSAMIC/snakemake_rules/annotation/varcaller_filter_tumor_normal.rule b/BALSAMIC/snakemake_rules/annotation/varcaller_filter_tumor_normal.rule
index 59e826187..b51b5f584 100644
--- a/BALSAMIC/snakemake_rules/annotation/varcaller_filter_tumor_normal.rule
+++ b/BALSAMIC/snakemake_rules/annotation/varcaller_filter_tumor_normal.rule
@@ -31,20 +31,22 @@ rule bcftools_filter_vardict_research_tumor_normal:
 bcftools view {input.vcf_snv_research} | \
 bcftools filter --threads {threads} --include 'INFO/GNOMADAF_popmax <= {params.pop_freq[0]} || INFO/GNOMADAF_popmax == \".\"' --soft-filter '{params.pop_freq[1]}' --mode '+' | \
 bcftools filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
-bcftools view -f PASS -o {output.vcf_pass_vardict}.temp -O z;
-
-tabix -p vcf -f {output.vcf_pass_vardict}.temp;
+bcftools view -f PASS -o {output.vcf_pass_vardict}.temp1 -O z;
 
 python {params.edit_vcf_script} \
---input_vcf {output.vcf_pass_vardict}.temp \
---output_vcf {output.vcf_pass_vardict} \
+--input_vcf {output.vcf_pass_vardict}.temp1 \
+--output_vcf {output.vcf_pass_vardict}.temp2 \
 --variant_caller {params.variant_caller};
 
+bgzip -@ {threads} -l 9 -c {output.vcf_pass_vardict}.temp2 > {output.vcf_pass_vardict}
+
 tabix -p vcf -f {output.vcf_pass_vardict};
 
 bcftools +counts {output.vcf_pass_vardict} > {output.bcftools_counts_research};
     
-rm {output.vcf_pass_vardict}.temp;
+rm {output.vcf_pass_vardict}.temp1;
+
+rm {output.vcf_pass_vardict}.temp2;
     """
 
 
@@ -107,20 +109,22 @@ rule bcftools_filter_TNscope_umi_research_tumor_normal:
 bcftools view  -f PASS,triallelic_site --threads {threads} {input.vcf_snv_research} | \
 bcftools filter --threads {threads} --include 'INFO/GNOMADAF_popmax <= {params.pop_freq[0]} || INFO/GNOMADAF_popmax == \".\"' --soft-filter '{params.pop_freq[1]}' --mode '+' | \
 bcftools filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
-bcftools view --threads {threads} -f PASS,triallelic_site -o {output.vcf_pass_tnscope_umi}.temp -O z;
-
-tabix -p vcf -f {output.vcf_pass_tnscope_umi}.temp;
+bcftools view --threads {threads} -f PASS,triallelic_site -o {output.vcf_pass_tnscope_umi}.temp1 -O z;
 
 python {params.edit_vcf_script} \
---input_vcf {output.vcf_pass_tnscope_umi}.temp \
---output_vcf {output.vcf_pass_tnscope_umi} \
+--input_vcf {output.vcf_pass_tnscope_umi}.temp1 \
+--output_vcf {output.vcf_pass_tnscope_umi}.temp2 \
 --variant_caller {params.variant_caller};
 
+bgzip -@ {threads} -l 9 -c {output.vcf_pass_tnscope_umi}.temp2 > {output.vcf_pass_tnscope_umi}
+
 tabix -p vcf -f {output.vcf_pass_tnscope_umi};
 
 bcftools +counts {output.vcf_pass_tnscope_umi} > {output.bcftools_counts_research};
 
-rm {output.vcf_pass_tnscope_umi}.temp;
+rm {output.vcf_pass_tnscope_umi}.temp1;
+
+rm {output.vcf_pass_tnscope_umi}.temp2;
     """
 
 
@@ -153,20 +157,22 @@ bcftools view {input.vcf_snv_clinical} | \
 bcftools filter --threads {threads} --include 'INFO/GNOMADAF_popmax <= {params.pop_freq[0]} || INFO/GNOMADAF_popmax == \".\"' --soft-filter '{params.pop_freq[1]}' --mode '+' | \
 bcftools filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
 bcftools filter --threads {threads} --include 'INFO/Frq <= {params.loqusdb_clinical_freq[0]} || INFO/Frq == \".\"' --soft-filter '{params.loqusdb_clinical_freq[1]}' --mode '+' |\
-bcftools view --threads {threads} -f PASS -o {output.vcf_pass_vardict}.temp -O z;
-
-tabix -p vcf -f {output.vcf_pass_vardict}.temp;
+bcftools view --threads {threads} -f PASS -o {output.vcf_pass_vardict}.temp1 -O z;
 
 python {params.edit_vcf_script} \
---input_vcf {output.vcf_pass_vardict}.temp \
---output_vcf {output.vcf_pass_vardict} \
+--input_vcf {output.vcf_pass_vardict}.temp1 \
+--output_vcf {output.vcf_pass_vardict}.temp2 \
 --variant_caller {params.variant_caller};
 
+bgzip -@ {threads} -l 9 -c {output.vcf_pass_vardict}.temp2 > {output.vcf_pass_vardict}
+
 tabix -p vcf -f {output.vcf_pass_vardict};
 
 bcftools +counts {output.vcf_pass_vardict} > {output.bcftools_counts_clinical};
 
-rm {output.vcf_pass_vardict}.temp;
+rm {output.vcf_pass_vardict}.temp1;
+
+rm {output.vcf_pass_vardict}.temp2;
     """
 
 
@@ -199,18 +205,20 @@ bcftools view  -f PASS,triallelic_site --threads {threads} {input.vcf_snv_clinic
 bcftools filter --threads {threads} --include 'INFO/GNOMADAF_popmax <= {params.pop_freq[0]} || INFO/GNOMADAF_popmax == \".\"' --soft-filter '{params.pop_freq[1]}' --mode '+' | \
 bcftools filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
 bcftools filter --threads {threads} --include 'INFO/Frq <= {params.loqusdb_clinical_freq[0]} || INFO/Frq == \".\"' --soft-filter '{params.loqusdb_clinical_freq[1]}' --mode '+' |\
-bcftools view --threads {threads} -f PASS,triallelic_site -o {output.vcf_pass_tnscope_umi}.temp -O z;
-
-tabix -p vcf -f {output.vcf_pass_tnscope_umi}.temp;
+bcftools view --threads {threads} -f PASS,triallelic_site -o {output.vcf_pass_tnscope_umi}.temp1 -O z;
 
 python {params.edit_vcf_script} \
---input_vcf {output.vcf_pass_tnscope_umi}.temp \
---output_vcf {output.vcf_pass_tnscope_umi} \
+--input_vcf {output.vcf_pass_tnscope_umi}.temp1 \
+--output_vcf {output.vcf_pass_tnscope_umi}.temp2 \
 --variant_caller {params.variant_caller};
 
+bgzip -@ {threads} -l 9 -c {output.vcf_pass_tnscope_umi}.temp2 > {output.vcf_pass_tnscope_umi}
+
 tabix -p vcf -f {output.vcf_pass_tnscope_umi};
 
 bcftools +counts {output.vcf_pass_tnscope_umi} > {output.bcftools_counts_clinical};
 
-rm {output.vcf_pass_tnscope_umi}.temp;
+rm {output.vcf_pass_tnscope_umi}.temp1;
+
+rm {output.vcf_pass_tnscope_umi}.temp2;
     """
diff --git a/BALSAMIC/snakemake_rules/annotation/varcaller_filter_tumor_only.rule b/BALSAMIC/snakemake_rules/annotation/varcaller_filter_tumor_only.rule
index 955ea2894..141585c60 100644
--- a/BALSAMIC/snakemake_rules/annotation/varcaller_filter_tumor_only.rule
+++ b/BALSAMIC/snakemake_rules/annotation/varcaller_filter_tumor_only.rule
@@ -31,20 +31,22 @@ rule bcftools_filter_vardict_research_tumor_only:
 bcftools view {input.vcf_snv_research} | \
 bcftools filter --threads {threads} --include 'INFO/GNOMADAF_popmax <= {params.pop_freq[0]} || INFO/GNOMADAF_popmax == \".\"' --soft-filter '{params.pop_freq[1]}' --mode '+' | \
 bcftools filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
-bcftools view --threads {threads} -f PASS -o {output.vcf_pass_vardict}.temp -O z;
-
-tabix -p vcf -f {output.vcf_pass_vardict}.temp;
+bcftools view --threads {threads} -f PASS -o {output.vcf_pass_vardict}.temp1 -O z;
 
 python {params.edit_vcf_script} \
---input_vcf {output.vcf_pass_vardict}.temp \
---output_vcf {output.vcf_pass_vardict} \
+--input_vcf {output.vcf_pass_vardict}.temp1 \
+--output_vcf {output.vcf_pass_vardict}.temp2 \
 --variant_caller {params.variant_caller};
 
+bgzip -@ {threads} -l 9 -c {output.vcf_pass_vardict}.temp2 > {output.vcf_pass_vardict}
+
 tabix -p vcf -f {output.vcf_pass_vardict};
 
 bcftools +counts {output.vcf_pass_vardict} > {output.bcftools_counts_research};
 
-rm {output.vcf_pass_vardict}.temp;
+rm {output.vcf_pass_vardict}.temp1;
+
+rm {output.vcf_pass_vardict}.temp2;
     """
 
 
@@ -107,20 +109,22 @@ rule bcftools_filter_TNscope_umi_research_tumor_only:
 bcftools view {input.vcf_snv_research} | \
 bcftools filter --include 'INFO/GNOMADAF_popmax <= {params.pop_freq[0]} || INFO/GNOMADAF_popmax == \".\"' --soft-filter '{params.pop_freq[1]}' --mode '+' | \
 bcftools filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
-bcftools view --threads {threads} -f PASS,triallelic_site -o {output.vcf_pass_tnscope_umi}.temp -O z;
-
-tabix -p vcf -f {output.vcf_pass_tnscope_umi}.temp;
+bcftools view --threads {threads} -f PASS,triallelic_site -o {output.vcf_pass_tnscope_umi}.temp1 -O z;
 
 python {params.edit_vcf_script} \
---input_vcf {output.vcf_pass_tnscope_umi}.temp \
---output_vcf {output.vcf_pass_tnscope_umi} \
+--input_vcf {output.vcf_pass_tnscope_umi}.temp1 \
+--output_vcf {output.vcf_pass_tnscope_umi}.temp2 \
 --variant_caller {params.variant_caller};
 
+bgzip -@ {threads} -l 9 -c {output.vcf_pass_tnscope_umi}.temp2 > {output.vcf_pass_tnscope_umi}
+
 tabix -p vcf -f {output.vcf_pass_tnscope_umi};
 
 bcftools +counts {output.vcf_pass_tnscope_umi} > {output.bcftools_counts_research};
     
-rm {output.vcf_pass_tnscope_umi}.temp;
+rm {output.vcf_pass_tnscope_umi}.temp1;
+
+rm {output.vcf_pass_tnscope_umi}.temp2;
     """
 
 
@@ -153,20 +157,22 @@ bcftools view {input.vcf_snv_clinical} | \
 bcftools filter --include 'INFO/GNOMADAF_popmax <= {params.pop_freq[0]} || INFO/GNOMADAF_popmax == \".\"' --soft-filter '{params.pop_freq[1]}' --mode '+' | \
 bcftools filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
 bcftools filter --threads {threads} --include 'INFO/Frq <= {params.loqusdb_clinical_freq[0]} || INFO/Frq == \".\"' --soft-filter '{params.loqusdb_clinical_freq[1]}' --mode '+' |\
-bcftools view --threads {threads} -f PASS -o {output.vcf_pass_vardict}.temp -O z;
-
-tabix -p vcf -f {output.vcf_pass_vardict}.temp;
+bcftools view --threads {threads} -f PASS -o {output.vcf_pass_vardict}.temp1 -O z;
 
 python {params.edit_vcf_script} \
---input_vcf {output.vcf_pass_vardict}.temp \
---output_vcf {output.vcf_pass_vardict} \
+--input_vcf {output.vcf_pass_vardict}.temp1 \
+--output_vcf {output.vcf_pass_vardict}.temp2 \
 --variant_caller {params.variant_caller};
 
+bgzip -@ {threads} -l 9 -c {output.vcf_pass_vardict}.temp2 > {output.vcf_pass_vardict}
+
 tabix -p vcf -f {output.vcf_pass_vardict};
 
 bcftools +counts {output.vcf_pass_vardict} > {output.bcftools_counts_clinical};
 
-rm {output.vcf_pass_vardict}.temp;
+rm {output.vcf_pass_vardict}.temp1;
+
+rm {output.vcf_pass_vardict}.temp2;
     """
 
 
@@ -199,18 +205,20 @@ bcftools view {input.vcf_snv_clinical} | \
 bcftools filter --include 'INFO/GNOMADAF_popmax <= {params.pop_freq[0]} || INFO/GNOMADAF_popmax == \".\"' --soft-filter '{params.pop_freq[1]}' --mode '+' | \
 bcftools filter --threads {threads} --include 'INFO/SWEGENAF <= {params.swegen_freq[0]} || INFO/SWEGENAF == \".\"' --soft-filter '{params.swegen_freq[1]}' --mode '+' |\
 bcftools filter --threads {threads} --include 'INFO/Frq <= {params.loqusdb_clinical_freq[0]} || INFO/Frq == \".\"' --soft-filter '{params.loqusdb_clinical_freq[1]}' --mode '+' |\
-bcftools view --threads {threads} -f PASS,triallelic_site -o {output.vcf_pass_tnscope_umi}.temp -O z;
-
-tabix -p vcf -f {output.vcf_pass_tnscope_umi}.temp;
+bcftools view --threads {threads} -f PASS,triallelic_site -o {output.vcf_pass_tnscope_umi}.temp1 -O z;
 
 python {params.edit_vcf_script} \
---input_vcf {output.vcf_pass_tnscope_umi}.temp \
---output_vcf {output.vcf_pass_tnscope_umi} \
+--input_vcf {output.vcf_pass_tnscope_umi}.temp1 \
+--output_vcf {output.vcf_pass_tnscope_umi}.temp2 \
 --variant_caller {params.variant_caller};
 
+bgzip -@ {threads} -l 9 -c {output.vcf_pass_tnscope_umi}.temp2 > {output.vcf_pass_tnscope_umi}
+
 tabix -p vcf -f {output.vcf_pass_tnscope_umi};
 
 bcftools +counts {output.vcf_pass_tnscope_umi} > {output.bcftools_counts_clinical};
 
-rm {output.vcf_pass_tnscope_umi}.temp;
+rm {output.vcf_pass_tnscope_umi}.temp1;
+
+rm {output.vcf_pass_tnscope_umi}.temp2;
     """
diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index e99ba6ca6..7da99d0d2 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -13,6 +13,7 @@ Changed:
 Fixed:
 ^^^^^^
 * triallelic_site in quality filter for SNV https://github.com/Clinical-Genomics/BALSAMIC/pull/1052
+* Compression of SNV, research and clinical, VCF files https://github.com/Clinical-Genomics/BALSAMIC/pull/1060 
 * `test_write_json` failing locally https://github.com/Clinical-Genomics/BALSAMIC/pull/1063
 * Container build and push via github actions by setting buildx `provenance` flag to false https://github.com/Clinical-Genomics/BALSAMIC/pull/1071
 * Added buildx to the submodule workflow https://github.com/Clinical-Genomics/BALSAMIC/pull/1072