diff --git a/.gitignore b/.gitignore
index 0ec05b6..9392b3d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -29,6 +29,8 @@ MANIFEST
 out*
 test.txt
 tmpout
+tests/test_*/*.vcf
+*.log
 
 # PyInstaller
 #  Usually these files are written by a python script from a template
diff --git a/CHANGES.md b/CHANGES.md
index 227193e..a95e73a 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,4 +1,6 @@
 
+## 1.2.1
+* updated documentation and README
 ## 1.2.0
 * Added json config paramter to accept filtering paramaters
 * removed commandline paramaters that are now read from config file
diff --git a/Dockerfile b/Dockerfile
index 596ba43..3b8fc51 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -3,7 +3,7 @@ USER root
 
 MAINTAINER  cgphelp@sanger.ac.uk
 
-ENV ANNOTATEVCF_VER '1.2.0'
+ENV ANNOTATEVCF_VER '1.2.1'
 
 # install system tools
 RUN apt-get -yq update
@@ -40,7 +40,7 @@ RUN pip3 install --install-option="--prefix=$CGP_OPT/python-lib" dist/$(ls -1 di
 FROM ubuntu:20.04
 
 LABEL uk.ac.sanger.cgp="Cancer Genome Project, Wellcome Sanger Institute" \
-      version="1.2.0" \
+      version="1.2.1" \
       description="Tool to perform vcf file annotation"
 
 ### security upgrades and cleanup
diff --git a/README.md b/README.md
index ebb903e..45ef501 100644
--- a/README.md
+++ b/README.md
@@ -41,13 +41,13 @@ Various exceptions can occur for malformed input files.
  * ```input_vcf.gz```  snv or indel vcf file annotated using [VAGrENT]
  * ```normal_panel.vcf.gz```  normal panel to tag germline variants [VAGrENT]
  * ```lof_genes.txt ``` list of known loss of function [LoF] genes along with previous gene symbols ( to make sure all gene synonyms were matched with input vcf)
- * ```consequence types``` lof consequence types to restrict driver gene annotations  
+ * ```filters.json``` filters to be applied during driver annotations ( see default file ```filters.josn``` in config  folder)
  * ```driver_mutations.tsv.gz``` tab separated driver mutations along with consequence type 
  * ```info.header``` vcf header INFO line 
 
 ### outputFormat
 
- * ```<input>.drv.vcf.gz ``` output vcf file with DRV info field and consequence type if known, LoF in case annotated using LoF gene list.
+ * ```<input>_drv.vcf.gz ``` output vcf file with DRV info field and consequence type if known, LoF in case annotated using LoF gene list.
 
 ## INSTALL
 Installing via `pip install`. Simply execute with the path to the compiled 'whl' found on the [release page][annotateVcf-releases]:
diff --git a/annotate/commandline.py b/annotate/commandline.py
index b81169c..ad9433e 100644
--- a/annotate/commandline.py
+++ b/annotate/commandline.py
@@ -29,8 +29,7 @@ def main():
                           default=None, help="vcf_file to annotate")
 
     optional.add_argument("-filters", "--vcf_filters", type=str, dest="vcf_filters", required=False,
-                          default=filters_json, help="Include vcf filters \
-                          configuration file in json (param:value) format \
+                          default=filters_json, help="Include vcf filters file in json format \
                           [please refer bcftools documentation for more details \
                            : http://samtools.github.io/bcftools/bcftools.html#expressions]")
 
@@ -38,7 +37,7 @@ def main():
                           default=None, help="normal panel file to flag germline variant sites")
 
     optional.add_argument("-g", "--lof_genes", type=str, dest="lof_genes", required=False,
-                          default=None, help="LoF gene name file to use annotations")
+                          default=None, help="Known LoF genes file to annotate LoF variants")
 
     optional.add_argument("-m", "--mutations", type=str, dest="mutations", required=False,
                           default=None, help="driver mutations file to use for driver variant annotations")
@@ -70,6 +69,5 @@ def main():
     with formatter.tempdir(outdir_path['outdir']) as base_dir:
         annotator.VcfAnnotator(my_formatter, base_dir)
 
-
 if __name__ == '__main__':
     main()
diff --git a/setup.py b/setup.py
index 8939e02..126ede2 100644
--- a/setup.py
+++ b/setup.py
@@ -3,7 +3,7 @@
 from setuptools import setup
 
 config = {
-    'version': '1.2.0',
+    'version': '1.2.1',
     'name': 'annotateVcf',
     'description': 'Tool to annotate and filter vcf files...',
     'author': 'Shriram Bhosle',
diff --git a/tests/test_output_no_vaf_vcf/input_genes.vcf b/tests/test_output_no_vaf_vcf/input_genes.vcf
deleted file mode 100644
index 11b5f03..0000000
--- a/tests/test_output_no_vaf_vcf/input_genes.vcf
+++ /dev/null
@@ -1,97 +0,0 @@
-##fileformat=VCFv4.1
-##FILTER=<ID=PASS,Description="All filters passed">
-##FILTER=<ID=DTH,Description="Less than 1/3 mutant alleles were >= 25 base quality">
-##FILTER=<ID=RP,Description="Coverage was less than 8 and no mutant alleles were found in the first 2/3 of a read (shifted 0.08 from the start and extended 0.08 more than 2/3 of the read length)">
-##FILTER=<ID=MN,Description="More than 0.05 of mutant alleles that were >= 15 base quality found in the matched normal">
-##FILTER=<ID=PT,Description="Mutant alleles all on one direction of read (1rd allowed on opposite strand) and in second half of the read. Second half of read contains the motif GGC[AT]G in sequenced orientation and the mean base quality of all bases after the motif was less than 20">
-##FILTER=<ID=MQ,Description="Mean mapping quality of the mutant allele reads was < 21">
-##FILTER=<ID=SR,Description="Position falls within a simple repeat using the supplied bed file">
-##FILTER=<ID=CR,Description="Position falls within a centromeric repeat using the supplied bed file">
-##FILTER=<ID=PH,Description="Mutant reads were on one strand (permitted proportion on other strand: 0.04), and mean mutant base quality was less than 21">
-##FILTER=<ID=HSD,Description="Position falls within a high sequencing depth region using the supplied bed file">
-##FILTER=<ID=GI,Description="Position falls within a germline indel using the supplied bed file">
-##FILTER=<ID=VUM,Description="Position has >= 3 mutant allele present in at least 1 percent unmatched normal samples in the unmatched VCF.">
-##FILTER=<ID=SE,Description="Coverage is >= 10 on each strand but mutant allele is only present on one strand">
-##FILTER=<ID=MNP,Description="Tumour sample mutant allele proportion - normal sample mutant allele proportion < 0.2">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=FAZ,Number=1,Type=Integer,Description="Reads presenting a A for this position, forward strand">
-##FORMAT=<ID=FCZ,Number=1,Type=Integer,Description="Reads presenting a C for this position, forward strand">
-##FORMAT=<ID=FGZ,Number=1,Type=Integer,Description="Reads presenting a G for this position, forward strand">
-##FORMAT=<ID=FTZ,Number=1,Type=Integer,Description="Reads presenting a T for this position, forward strand">
-##FORMAT=<ID=RAZ,Number=1,Type=Integer,Description="Reads presenting a A for this position, reverse strand">
-##FORMAT=<ID=RCZ,Number=1,Type=Integer,Description="Reads presenting a C for this position, reverse strand">
-##FORMAT=<ID=RGZ,Number=1,Type=Integer,Description="Reads presenting a G for this position, reverse strand">
-##FORMAT=<ID=RTZ,Number=1,Type=Integer,Description="Reads presenting a T for this position, reverse strand">
-##FORMAT=<ID=PM,Number=1,Type=Float,Description="Proportion of mut allele">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##INFO=<ID=MP,Number=1,Type=Float,Description="Sum of CaVEMan somatic genotype probabilities">
-##INFO=<ID=GP,Number=1,Type=Float,Description="Sum of CaVEMan germline genotype probabilities">
-##INFO=<ID=TG,Number=1,Type=String,Description="Most probable genotype as called by CaVEMan">
-##INFO=<ID=TP,Number=1,Type=Float,Description="Probability of most probable genotype as called by CaVEMan">
-##INFO=<ID=SG,Number=1,Type=String,Description="2nd most probable genotype as called by CaVEMan">
-##INFO=<ID=SP,Number=1,Type=Float,Description="Probability of 2nd most probable genotype as called by CaVEMan">
-##INFO=<ID=DS,Number=.,Type=String,Description="DBSnp ID of known SNP">
-##INFO=<ID=SNP,Number=0,Type=Flag,Description="Position matches a dbSNP entry using the supplied bed file">
-##INFO=<ID=ASRD,Number=1,Type=Float,Description="A soft flag median (read length adjusted) alignment score of reads showing the variant allele">
-##INFO=<ID=CLPM,Number=1,Type=Float,Description="A soft flag median number of soft clipped bases in variant supporting reads">
-##INFO=<ID=ASMD,Number=1,Type=Float,Description="A soft flag median alignement score of reads showing the variant allele">
-##INFO=<ID=VD,Number=1,Type=String,Description="Vagrent Default Annotation">
-##INFO=<ID=VW,Number=1,Type=String,Description="Vagrent Most Deleterious Annotation">
-##INFO=<ID=VT,Number=1,Type=String,Description="Variant type based on the Vagrent Default Annotation">
-##INFO=<ID=VC,Number=.,Type=String,Description="Variant consequence based on the Vagrent Default Annotation">
-##SAMPLE=<ID=NORMAL,Description="Normal",Accession=.,Platform=ILLUMINA,Protocol=WGS,SampleName=WTSI-COLO_005_b,Source=.>
-##SAMPLE=<ID=TUMOUR,Description="Tumour",Accession=.,Platform=ILLUMINA,Protocol=WGS,SampleName=WTSI-COLO_005_1pre,Source=.>
-##cavemanVersion=1.14.1
-##cgpAnalysisProc_20200116.1=5524663
-##contig=<ID=chr1,assembly=NCBI38,length=248956422,species=Human>
-##contig=<ID=chr2,assembly=NCBI38,length=242193529,species=Human>
-##contig=<ID=chr3,assembly=NCBI38,length=198295559,species=Human>
-##contig=<ID=chr4,assembly=NCBI38,length=190214555,species=Human>
-##contig=<ID=chr5,assembly=NCBI38,length=181538259,species=Human>
-##contig=<ID=chr6,assembly=NCBI38,length=170805979,species=Human>
-##contig=<ID=chr7,assembly=NCBI38,length=159345973,species=Human>
-##contig=<ID=chr8,assembly=NCBI38,length=145138636,species=Human>
-##contig=<ID=chr9,assembly=NCBI38,length=138394717,species=Human>
-##contig=<ID=chr10,assembly=NCBI38,length=133797422,species=Human>
-##contig=<ID=chr11,assembly=NCBI38,length=135086622,species=Human>
-##contig=<ID=chr12,assembly=NCBI38,length=133275309,species=Human>
-##contig=<ID=chr13,assembly=NCBI38,length=114364328,species=Human>
-##contig=<ID=chr14,assembly=NCBI38,length=107043718,species=Human>
-##contig=<ID=chr15,assembly=NCBI38,length=101991189,species=Human>
-##contig=<ID=chr16,assembly=NCBI38,length=90338345,species=Human>
-##contig=<ID=chr17,assembly=NCBI38,length=83257441,species=Human>
-##contig=<ID=chr18,assembly=NCBI38,length=80373285,species=Human>
-##contig=<ID=chr19,assembly=NCBI38,length=58617616,species=Human>
-##contig=<ID=chr20,assembly=NCBI38,length=64444167,species=Human>
-##contig=<ID=chr21,assembly=NCBI38,length=46709983,species=Human>
-##contig=<ID=chr22,assembly=NCBI38,length=50818468,species=Human>
-##contig=<ID=chrX,assembly=NCBI38,length=156040895,species=Human>
-##contig=<ID=chrY,assembly=NCBI38,length=57227415,species=Human>
-##contig=<ID=chrM,assembly=NCBI38,length=16569,species=Human>
-##fileDate=20200115
-##reference=/lustre/scratch119/casm/team78pipelines/canpipe/live/data/analysis/2126_2577635/CaVEMan/genome.fa
-##source_20200119.1=AnnotateVcf.pl
-##vcfProcessLog=<InputVCF=<.>,InputVCFSource=<CaVEMan>,InputVCFParam=<REF_BIAS=0.95,SNP_CUTOFF=0.95,MUT_CUTOFF=0.8,NORMAL_CONTAMINATION=0,PRIOR_SNP_RATE=0.0001,PRIOR_MUT_RATE=6e-06>>
-##vcfProcessLog_20200116.1=<InputVCF=<split.vcf.1>,InputVCFSource=<FlagCaVEManVCF.pl>,InputVCFVer=<1.8.9>,InputVCFParam=<v=flag.to.vcf.convert.ini,o=flagged_split.vcf.1,ab=.,umv=unmatched_v5,idx=.,l=2000,h=.,sp=.,s=HUMAN,n=2543786.bam,c=flag.vcf.config.ini,m=2577635.bam,t=WGS,ref=genome.fa.fai,loud=.,f=split.vcf.1,g=2577635.germline.bed.gz,b=flagging,p=5524663,sa=.>>
-##vcfProcessLog_20200119.1=<InputVCF=<>,InputVCFSource=<AnnotateVcf.pl>,InputVCFVer=<3.5.2>,InputVCFParam=<species=Human,output=/lustre/scratch119/casm/team78pipelines/canpipe/live/data/analysis/2126_2577635/Vagrent_CaVEMan/WTSI-COLO_005_1pre.vcf,tabix=1,input=/lustre/scratch119/casm/team78pipelines/canpipe/live/data/stage/2126_2577635/2577635.caveman_c.flag.vcf.gz,assembly=NCBI38,cache=/lustre/scratch119/casm/team78pipelines/canpipe/live/ref/human/GRCh38_full_analysis_set_plus_decoy_hla/vagrent/e91/vagrent.cache.gz>>
-##bcftools_viewVersion=1.12+htslib-1.12
-##bcftools_viewCommand=view -R lof_pos.txt /lustre/scratch117/casm/team215/sb43/organoid_analysis/WGS/p2126/out_vafcorrect//WTSI-COLO_005_1pre.caveman_c.annot.vcf.gz; Date=Tue Mar 30 14:23:07 2021
-##INFO=<ID=DRV,Number=.,Type=String,Description="Driver Variant Class">
-##bcftools_annotateVersion=1.12+htslib-1.12
-##bcftools_annotateCommand=annotate -a test_output/tmpdtvu0kq9/genome.tab.gz -i '(FILTER="PASS" ) && ( INFO/VC="stop_lost,start_lost,ess_splice,frameshift,nonsense")' -h /nfs/users/nfs_s/sb43/scripts/annotatevcf_github/annotate/config/info.header -c CHROM,FROM,TO,INFO/DRV input.vcf.gz; Date=Tue Mar 30 16:55:58 2021
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOUR
-chr1	161193208	3883f734-37d6-11ea-a6a1-4d80907df7c2	C	A	.	PASS	DP=63;MP=1;GP=1.5e-07;TG=CC/ACC;TP=0.99;SG=CC/AAC;SP=0.014;ASRD=0.97;CLPM=0;ASMD=146;VT=Sub;VD=ADAMTS4|CCDS1223.1|r.2340+5g>u|c.1911+5G>T|p.?|protein_coding:CDS:extended_cis_splice_site:substitution:splice_site_variant:transcript_variant|SO:0000010:SO:0000316:SO:0001993:SO:1000002:SO:0001629:SO:0001576;VC=ess_splice;VW=ADAMTS4|CCDS1223.1|r.2340+5g>u|c.1911+5G>T|p.?|protein_coding:CDS:extended_cis_splice_site:substitution:splice_site_variant:transcript_variant|SO:0000010:SO:0000316:SO:0001993:SO:1000002:SO:0001629:SO:0001576;DRV=LoF	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:0:12:0:0:0:15:0:0:0	0|1:9:12:0:0:5:9:1:0:0.39
-chr1	219210652	38868fa8-37d6-11ea-a6a1-4d80907df7c2	G	A	.	PASS	DP=91;MP=1;GP=2.6e-13;TG=GG/AAG;TP=1;SG=GG/AGG;SP=3.4e-06;ASRD=0.92;CLPM=0;ASMD=139.5;VT=Sub;VD=LYPLAL1|CCDS1522.1|r.524+5g>a|c.477+5G>A|p.?|protein_coding:CDS:extended_cis_splice_site:substitution:splice_site_variant:transcript_variant|SO:0000010:SO:0000316:SO:0001993:SO:1000002:SO:0001629:SO:0001576;VC=ess_splice;VW=LYPLAL1|CCDS1522.1|r.524+5g>a|c.477+5G>A|p.?|protein_coding:CDS:extended_cis_splice_site:substitution:splice_site_variant:transcript_variant|SO:0000010:SO:0000316:SO:0001993:SO:1000002:SO:0001629:SO:0001576;DRV=LoF	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:0:0:26:0:0:0:21:0:0	0|1:17:1:7:0:13:0:6:0:0.68
-chr1	247934046	3887f190-37d6-11ea-a6a1-4d80907df7c2	C	A	.	PASS	DP=76;MP=1;GP=1.3e-13;TG=CC/ACC;TP=1;SG=CC/AAC;SP=0.0014;ASRD=0.97;CLPM=0;ASMD=146;VT=Sub;VD=OR2AJ1|ENST00000318244|r.580c>a|c.278C>A|p.S93*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;VC=nonsense;VW=OR2AJ1|ENST00000318244|r.580c>a|c.278C>A|p.S93*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;DRV=LoF	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:0:22:0:0:0:26:0:0:0	0|1:2:9:0:0:7:10:0:0:0.32
-chr10	113160663	38932966-37d6-11ea-a6a1-4d80907df7c2	C	T	.	PASS	DP=72;MP=1;GP=9.3e-10;TG=CC/CCT;TP=0.52;SG=CC/CTT;SP=0.48;ASRD=0.97;CLPM=0;ASMD=146;VT=Sub;VD=TCF7L2|CCDS53577.1|r.1713c>u|c.1363C>T|p.R455*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;VC=nonsense;VW=TCF7L2|CCDS53577.1|r.1713c>u|c.1363C>T|p.R455*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;DRV=LoF	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:0:17:0:0:1:17:0:0:0	0|1:0:13:0:8:0:6:0:10:0.49
-chr13	43888891	38b522aa-37d6-11ea-a6a1-4d80907df7c2	G	T	.	PASS	DP=89;MP=1;GP=2e-12;TG=GG/GGGT;TP=1;SG=GG/GGTT;SP=1.6e-05;ASRD=0.93;CLPM=0;ASMD=141;VT=Sub;VD=LACC1|CCDS9391.1|r.1527g>u|c.1042G>T|p.E348*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;VC=nonsense;VW=LACC1|CCDS9391.1|r.1527g>u|c.1042G>T|p.E348*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;DRV=LoF	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:0:0:23:0:0:0:21:0:0	0|1:0:0:22:3:0:0:17:3:0.13
-chr15	44715437	38c39ba0-37d6-11ea-a6a1-4d80907df7c2	C	T	.	PASS	DP=77;MP=1;GP=6.8e-14;TG=CC/TT;TP=1;SG=CC/CT;SP=6.5e-06;ASRD=0.97;CLPM=0;ASMD=146;VT=Sub;VD=B2M|CCDS10113.1|r.152c>u|c.82C>T|p.Q28*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;VC=nonsense;VW=B2M|CCDS10113.1|r.152c>u|c.82C>T|p.Q28*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;DRV=LoF	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:0:33:0:0:0:16:1:0:0	1|1:0:0:0:7:0:1:0:19:0.96
-chr18	56686854	38d994dc-37d6-11ea-a6a1-4d80907df7c2	G	T	.	PASS	DP=69;MP=1;GP=1.2e-13;TG=GG/GT;TP=1;SG=GT/GT;SP=1.2e-13;ASRD=0.87;CLPM=0;ASMD=131;VT=Sub;VD=WDR7|CCDS11962.1|r.809-1g>u|c.598-1G>T|p.?|protein_coding:CDS:extended_cis_splice_site:substitution:splice_site_variant:transcript_variant|SO:0000010:SO:0000316:SO:0001993:SO:1000002:SO:0001629:SO:0001576;VC=ess_splice;VW=WDR7|CCDS11962.1|r.809-1g>u|c.598-1G>T|p.?|protein_coding:CDS:extended_cis_splice_site:substitution:splice_site_variant:transcript_variant|SO:0000010:SO:0000316:SO:0001993:SO:1000002:SO:0001629:SO:0001576;DRV=LoF	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:0:0:29:0:0:0:19:0:0	0|1:0:0:6:7:1:0:2:5:0.57
-chr19	45821379	38ddcfca-37d6-11ea-a6a1-4d80907df7c2	C	A	.	PASS	DP=51;MP=1;GP=2.3e-06;TG=CC/AAC;TP=0.99;SG=CC/ACC;SP=0.01;ASRD=0.93;CLPM=0;ASMD=141;VT=Sub;VD=SYMPK|CCDS12676.2|r.3138+5g>u|c.2893+5G>T|p.?|protein_coding:CDS:extended_cis_splice_site:substitution:splice_site_variant:transcript_variant|SO:0000010:SO:0000316:SO:0001993:SO:1000002:SO:0001629:SO:0001576;VC=ess_splice;VW=SYMPK|CCDS12676.2|r.3138+5g>u|c.2893+5G>T|p.?|protein_coding:CDS:extended_cis_splice_site:substitution:splice_site_variant:transcript_variant|SO:0000010:SO:0000316:SO:0001993:SO:1000002:SO:0001629:SO:0001576;DRV=LoF	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:0:14:0:0:0:9:0:0:0	0|1:8:5:0:0:9:6:0:0:0.61
-chr2	1453776	38df3004-37d6-11ea-a6a1-4d80907df7c2	C	T	.	PASS	DP=71;MP=1;GP=7.7e-12;TG=CC/CCTT;TP=0.94;SG=CC/CCCT;SP=0.056;ASRD=0.97;CLPM=0;ASMD=146;VT=Sub;VD=TPO|CCDS1643.1|r.656c>u|c.565C>T|p.R189*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;VC=nonsense;VW=TPO|CCDS1643.1|r.656c>u|c.565C>T|p.R189*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;DRV=LoF	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:0:25:0:0:0:17:0:0:0	0|1:0:9:0:6:0:7:0:7:0.45
-chr2	165901790	38f5dd86-37d6-11ea-a6a1-4d80907df7c2	G	A	.	PASS	DP=81;MP=1;GP=1.8e-12;TG=GG/AAG;TP=1;SG=GG/AGG;SP=1.6e-05;ASRD=0.97;CLPM=0;ASMD=146;VT=Sub;VD=TTC21B|CCDS33315.1|r.2827c>u|c.2689C>T|p.Q897*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;VC=nonsense;VW=TTC21B|CCDS33315.1|r.2827c>u|c.2689C>T|p.Q897*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;DRV=LoF	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:0:0:22:0:0:0:22:0:0	0|1:15:0:7:0:11:0:4:0:0.7
-chr2	178775881	38f67ec6-37d6-11ea-a6a1-4d80907df7c2	C	A	.	PASS	DP=67;MP=1;GP=4.2e-10;TG=CC/AACC;TP=0.98;SG=CC/ACCC;SP=0.013;ASRD=0.93;CLPM=0;ASMD=141;VT=Sub;VD=TTN|CCDS59435.1|r.6208g>u|c.5983G>T|p.E1995*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;VC=nonsense;VW=TTN|CCDS59435.1|r.6208g>u|c.5983G>T|p.E1995*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;DRV=LoF	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:0:18:0:0:0:18:0:0:0	0|1:10:6:0:0:5:10:0:0:0.48
-chr4	47645090	392fb844-37d6-11ea-a6a1-4d80907df7c2	T	A	.	PASS	DP=71;MP=1;GP=1.4e-09;TG=TT/ATT;TP=1;SG=TT/TTT;SP=1.3e-05;ASRD=0.97;CLPM=0;ASMD=146;VT=Sub;VD=CORIN|CCDS3477.1|r.1948a>u|c.1948A>T|p.K650*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;VC=nonsense;VW=CORIN|CCDS3477.1|r.1948a>u|c.1948A>T|p.K650*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;DRV=LoF	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:0:0:0:18:0:0:0:16:0	0|1:3:0:0:19:3:0:0:12:0.16
-chr5	17634694	393ed4e6-37d6-11ea-a6a1-4d80907df7c2	C	T	.	PASS	DP=85;MP=1;GP=1.9e-12;TG=CC/CCT;TP=1;SG=CC/CTT;SP=4.3e-06;ASRD=0.97;CLPM=0;ASMD=146;VT=Sub;VD=AC233724.12|ENST00000512227|r.235c>u|c.235C>T|p.Q79*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;VC=nonsense;VW=AC233724.12|ENST00000512227|r.235c>u|c.235C>T|p.Q79*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;DRV=LoF	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:0:23:0:0:0:21:0:0:0	0|1:0:10:0:7:0:20:0:4:0.27
-chr5	112815507	3948d8a6-37d6-11ea-a6a1-4d80907df7c2	C	T	.	PASS	DP=74;MP=1;GP=3.8e-15;TG=CC/TT;TP=1;SG=CC/CT;SP=0.00055;ASRD=0.97;CLPM=0;ASMD=146;VT=Sub;VD=APC|CCDS4107.1|r.903c>u|c.847C>T|p.R283*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;VC=nonsense;VW=APC|CCDS4107.1|r.903c>u|c.847C>T|p.R283*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;DRV=LoF	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:0:28:0:0:0:25:0:0:0	1|1:0:0:0:11:0:1:0:9:0.95
-chrX	135545510	398ea07a-37d6-11ea-a6a1-4d80907df7c2	A	T	.	PASS	DP=84;MP=1;GP=2.8e-11;TG=AA/AAAT;TP=1;SG=AA/AATT;SP=2.3e-05;ASRD=0.95;CLPM=0;ASMD=143.5;VT=Sub;VD=INTS6L|CCDS35401.1|r.611a>u|c.277A>T|p.R93*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;VC=nonsense;VW=INTS6L|CCDS35401.1|r.611a>u|c.277A>T|p.R93*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;DRV=LoF	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:18:0:0:0:22:0:0:0:0	0|1:18:0:0:3:20:0:0:3:0.14
diff --git a/tests/test_output_no_vaf_vcf/input_genes_lof.vcf b/tests/test_output_no_vaf_vcf/input_genes_lof.vcf
deleted file mode 100644
index ea73295..0000000
--- a/tests/test_output_no_vaf_vcf/input_genes_lof.vcf
+++ /dev/null
@@ -1,84 +0,0 @@
-##fileformat=VCFv4.1
-##FILTER=<ID=PASS,Description="All filters passed">
-##FILTER=<ID=DTH,Description="Less than 1/3 mutant alleles were >= 25 base quality">
-##FILTER=<ID=RP,Description="Coverage was less than 8 and no mutant alleles were found in the first 2/3 of a read (shifted 0.08 from the start and extended 0.08 more than 2/3 of the read length)">
-##FILTER=<ID=MN,Description="More than 0.05 of mutant alleles that were >= 15 base quality found in the matched normal">
-##FILTER=<ID=PT,Description="Mutant alleles all on one direction of read (1rd allowed on opposite strand) and in second half of the read. Second half of read contains the motif GGC[AT]G in sequenced orientation and the mean base quality of all bases after the motif was less than 20">
-##FILTER=<ID=MQ,Description="Mean mapping quality of the mutant allele reads was < 21">
-##FILTER=<ID=SR,Description="Position falls within a simple repeat using the supplied bed file">
-##FILTER=<ID=CR,Description="Position falls within a centromeric repeat using the supplied bed file">
-##FILTER=<ID=PH,Description="Mutant reads were on one strand (permitted proportion on other strand: 0.04), and mean mutant base quality was less than 21">
-##FILTER=<ID=HSD,Description="Position falls within a high sequencing depth region using the supplied bed file">
-##FILTER=<ID=GI,Description="Position falls within a germline indel using the supplied bed file">
-##FILTER=<ID=VUM,Description="Position has >= 3 mutant allele present in at least 1 percent unmatched normal samples in the unmatched VCF.">
-##FILTER=<ID=SE,Description="Coverage is >= 10 on each strand but mutant allele is only present on one strand">
-##FILTER=<ID=MNP,Description="Tumour sample mutant allele proportion - normal sample mutant allele proportion < 0.2">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=FAZ,Number=1,Type=Integer,Description="Reads presenting a A for this position, forward strand">
-##FORMAT=<ID=FCZ,Number=1,Type=Integer,Description="Reads presenting a C for this position, forward strand">
-##FORMAT=<ID=FGZ,Number=1,Type=Integer,Description="Reads presenting a G for this position, forward strand">
-##FORMAT=<ID=FTZ,Number=1,Type=Integer,Description="Reads presenting a T for this position, forward strand">
-##FORMAT=<ID=RAZ,Number=1,Type=Integer,Description="Reads presenting a A for this position, reverse strand">
-##FORMAT=<ID=RCZ,Number=1,Type=Integer,Description="Reads presenting a C for this position, reverse strand">
-##FORMAT=<ID=RGZ,Number=1,Type=Integer,Description="Reads presenting a G for this position, reverse strand">
-##FORMAT=<ID=RTZ,Number=1,Type=Integer,Description="Reads presenting a T for this position, reverse strand">
-##FORMAT=<ID=PM,Number=1,Type=Float,Description="Proportion of mut allele">
-##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
-##INFO=<ID=MP,Number=1,Type=Float,Description="Sum of CaVEMan somatic genotype probabilities">
-##INFO=<ID=GP,Number=1,Type=Float,Description="Sum of CaVEMan germline genotype probabilities">
-##INFO=<ID=TG,Number=1,Type=String,Description="Most probable genotype as called by CaVEMan">
-##INFO=<ID=TP,Number=1,Type=Float,Description="Probability of most probable genotype as called by CaVEMan">
-##INFO=<ID=SG,Number=1,Type=String,Description="2nd most probable genotype as called by CaVEMan">
-##INFO=<ID=SP,Number=1,Type=Float,Description="Probability of 2nd most probable genotype as called by CaVEMan">
-##INFO=<ID=DS,Number=.,Type=String,Description="DBSnp ID of known SNP">
-##INFO=<ID=SNP,Number=0,Type=Flag,Description="Position matches a dbSNP entry using the supplied bed file">
-##INFO=<ID=ASRD,Number=1,Type=Float,Description="A soft flag median (read length adjusted) alignment score of reads showing the variant allele">
-##INFO=<ID=CLPM,Number=1,Type=Float,Description="A soft flag median number of soft clipped bases in variant supporting reads">
-##INFO=<ID=ASMD,Number=1,Type=Float,Description="A soft flag median alignement score of reads showing the variant allele">
-##INFO=<ID=VD,Number=1,Type=String,Description="Vagrent Default Annotation">
-##INFO=<ID=VW,Number=1,Type=String,Description="Vagrent Most Deleterious Annotation">
-##INFO=<ID=VT,Number=1,Type=String,Description="Variant type based on the Vagrent Default Annotation">
-##INFO=<ID=VC,Number=.,Type=String,Description="Variant consequence based on the Vagrent Default Annotation">
-##SAMPLE=<ID=NORMAL,Description="Normal",Accession=.,Platform=ILLUMINA,Protocol=WGS,SampleName=WTSI-COLO_005_b,Source=.>
-##SAMPLE=<ID=TUMOUR,Description="Tumour",Accession=.,Platform=ILLUMINA,Protocol=WGS,SampleName=WTSI-COLO_005_1pre,Source=.>
-##cavemanVersion=1.14.1
-##cgpAnalysisProc_20200116.1=5524663
-##contig=<ID=chr1,assembly=NCBI38,length=248956422,species=Human>
-##contig=<ID=chr2,assembly=NCBI38,length=242193529,species=Human>
-##contig=<ID=chr3,assembly=NCBI38,length=198295559,species=Human>
-##contig=<ID=chr4,assembly=NCBI38,length=190214555,species=Human>
-##contig=<ID=chr5,assembly=NCBI38,length=181538259,species=Human>
-##contig=<ID=chr6,assembly=NCBI38,length=170805979,species=Human>
-##contig=<ID=chr7,assembly=NCBI38,length=159345973,species=Human>
-##contig=<ID=chr8,assembly=NCBI38,length=145138636,species=Human>
-##contig=<ID=chr9,assembly=NCBI38,length=138394717,species=Human>
-##contig=<ID=chr10,assembly=NCBI38,length=133797422,species=Human>
-##contig=<ID=chr11,assembly=NCBI38,length=135086622,species=Human>
-##contig=<ID=chr12,assembly=NCBI38,length=133275309,species=Human>
-##contig=<ID=chr13,assembly=NCBI38,length=114364328,species=Human>
-##contig=<ID=chr14,assembly=NCBI38,length=107043718,species=Human>
-##contig=<ID=chr15,assembly=NCBI38,length=101991189,species=Human>
-##contig=<ID=chr16,assembly=NCBI38,length=90338345,species=Human>
-##contig=<ID=chr17,assembly=NCBI38,length=83257441,species=Human>
-##contig=<ID=chr18,assembly=NCBI38,length=80373285,species=Human>
-##contig=<ID=chr19,assembly=NCBI38,length=58617616,species=Human>
-##contig=<ID=chr20,assembly=NCBI38,length=64444167,species=Human>
-##contig=<ID=chr21,assembly=NCBI38,length=46709983,species=Human>
-##contig=<ID=chr22,assembly=NCBI38,length=50818468,species=Human>
-##contig=<ID=chrX,assembly=NCBI38,length=156040895,species=Human>
-##contig=<ID=chrY,assembly=NCBI38,length=57227415,species=Human>
-##contig=<ID=chrM,assembly=NCBI38,length=16569,species=Human>
-##fileDate=20200115
-##reference=/lustre/scratch119/casm/team78pipelines/canpipe/live/data/analysis/2126_2577635/CaVEMan/genome.fa
-##source_20200119.1=AnnotateVcf.pl
-##vcfProcessLog=<InputVCF=<.>,InputVCFSource=<CaVEMan>,InputVCFParam=<REF_BIAS=0.95,SNP_CUTOFF=0.95,MUT_CUTOFF=0.8,NORMAL_CONTAMINATION=0,PRIOR_SNP_RATE=0.0001,PRIOR_MUT_RATE=6e-06>>
-##vcfProcessLog_20200116.1=<InputVCF=<split.vcf.1>,InputVCFSource=<FlagCaVEManVCF.pl>,InputVCFVer=<1.8.9>,InputVCFParam=<v=flag.to.vcf.convert.ini,o=flagged_split.vcf.1,ab=.,umv=unmatched_v5,idx=.,l=2000,h=.,sp=.,s=HUMAN,n=2543786.bam,c=flag.vcf.config.ini,m=2577635.bam,t=WGS,ref=genome.fa.fai,loud=.,f=split.vcf.1,g=2577635.germline.bed.gz,b=flagging,p=5524663,sa=.>>
-##vcfProcessLog_20200119.1=<InputVCF=<>,InputVCFSource=<AnnotateVcf.pl>,InputVCFVer=<3.5.2>,InputVCFParam=<species=Human,output=/lustre/scratch119/casm/team78pipelines/canpipe/live/data/analysis/2126_2577635/Vagrent_CaVEMan/WTSI-COLO_005_1pre.vcf,tabix=1,input=/lustre/scratch119/casm/team78pipelines/canpipe/live/data/stage/2126_2577635/2577635.caveman_c.flag.vcf.gz,assembly=NCBI38,cache=/lustre/scratch119/casm/team78pipelines/canpipe/live/ref/human/GRCh38_full_analysis_set_plus_decoy_hla/vagrent/e91/vagrent.cache.gz>>
-##bcftools_viewVersion=1.12+htslib-1.12
-##bcftools_viewCommand=view -R lof_pos.txt /lustre/scratch117/casm/team215/sb43/organoid_analysis/WGS/p2126/out_vafcorrect//WTSI-COLO_005_1pre.caveman_c.annot.vcf.gz; Date=Tue Mar 30 14:23:07 2021
-##INFO=<ID=DRV,Number=.,Type=String,Description="Driver Variant Class">
-##bcftools_annotateVersion=1.12+htslib-1.12
-##bcftools_annotateCommand=annotate -a test_output/tmpdtvu0kq9/genome.tab.gz -i '(FILTER="PASS" ) && ( INFO/VC="stop_lost,start_lost,ess_splice,frameshift,nonsense")' -h /nfs/users/nfs_s/sb43/scripts/annotatevcf_github/annotate/config/info.header -c CHROM,FROM,TO,INFO/DRV input.vcf.gz; Date=Tue Mar 30 16:55:58 2021
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	NORMAL	TUMOUR
-chr15	44715437	38c39ba0-37d6-11ea-a6a1-4d80907df7c2	C	T	.	PASS	DP=77;MP=1;GP=6.8e-14;TG=CC/TT;TP=1;SG=CC/CT;SP=6.5e-06;ASRD=0.97;CLPM=0;ASMD=146;VT=Sub;VD=B2M|CCDS10113.1|r.152c>u|c.82C>T|p.Q28*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;VC=nonsense;VW=B2M|CCDS10113.1|r.152c>u|c.82C>T|p.Q28*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;DRV=LoF	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:0:33:0:0:0:16:1:0:0	1|1:0:0:0:7:0:1:0:19:0.96
-chr5	112815507	3948d8a6-37d6-11ea-a6a1-4d80907df7c2	C	T	.	PASS	DP=74;MP=1;GP=3.8e-15;TG=CC/TT;TP=1;SG=CC/CT;SP=0.00055;ASRD=0.97;CLPM=0;ASMD=146;VT=Sub;VD=APC|CCDS4107.1|r.903c>u|c.847C>T|p.R283*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;VC=nonsense;VW=APC|CCDS4107.1|r.903c>u|c.847C>T|p.R283*|protein_coding:exon:CDS:substitution:codon_variant:stop_gained|SO:0000010:SO:0000147:SO:0000316:SO:1000002:SO:0001581:SO:0001587;DRV=LoF	GT:FAZ:FCZ:FGZ:FTZ:RAZ:RCZ:RGZ:RTZ:PM	0|0:0:28:0:0:0:25:0:0:0	1|1:0:0:0:11:0:1:0:9:0.95