diff --git a/bin/CramConversion.sh b/bin/CramConversion.sh
old mode 100644
new mode 100755
diff --git a/bin/checkDataLimitGroups.sh b/bin/checkDataLimitGroups.sh
old mode 100644
new mode 100755
diff --git a/bin/checkValidationNGS_DNA_v5.sh b/bin/checkValidationNGS_DNA_v5.sh
old mode 100644
new mode 100755
diff --git a/bin/compareWithVKGL_gatk4.sh b/bin/compareWithVKGL_gatk4.sh
index 7771290..451f8fa 100755
--- a/bin/compareWithVKGL_gatk4.sh
+++ b/bin/compareWithVKGL_gatk4.sh
@@ -98,36 +98,32 @@ function giabvshc(){
 		echo "comparing ${type}: ${sampleName}vsHC"
 		## sample vs HC callset (precision)
 		# shellcheck disable=SC2154
-		gatk VariantEval \
-		-R "${refGenome}" \
-		-O "${outputFolder}/tmp/precision-${sampleName}vsHC_union.${type}.vcf" \
-		--eval "${outputFolder}/tmp/${sampleName}_${type}.union.20bp_filtered.vcf" \
-		--comp "/apps/data/NIST/${namingConvention}/GIAB_HC.${type}_20bp.vcf"
+		"${EBROOTNGSMINUTILS}/bin/vcf-compare-precision-sensitivity.sh" \
+		-1 "${outputFolder}/tmp/${sampleName}_${type}.union.20bp_filtered.vcf" \
+		-2 "/apps/data/NIST/${namingConvention}/GIAB_HC.${type}_20bp.vcf" \
+		-o "${outputFolder}/tmp/precision-${sampleName}vsHC_union_${type}/"
+
 
 		if [[ "${firstLine}" == "false" ]]
 		then
-			## print header too
-			head -4 "${outputFolder}/tmp/precision-${sampleName}vsHC_union.${type}.vcf" | tail -1 | awk '{OFS="\t"}{print "measurement","Type",$6,$7,$8,$9,$10,$11,"FinalConcordance"}' > "${outputFolder}/precision_output.txt"
+			awk '{if(NR==1){print "Measurement\tType\t"$0}}' "${outputFolder}/tmp/precision-${sampleName}vsHC_union_${type}/comparison.txt" > "${outputFolder}/precision_output.txt"
 		fi
-		head -5 "${outputFolder}/tmp/precision-${sampleName}vsHC_union.${type}.vcf" | tail -1 | awk -v type="${type}" '{OFS="\t"}{print "precision",type,$6,$7,$8,$9,$10,$11,(($10/$6)*100)}' >> "${outputFolder}/precision_output.txt"
-	
-		echo "comparing ${type}: HCvs${sampleName}"
+		awk -v type=${type} '{if(NR>1){print "precision\t"type"\t"$0}}' "${outputFolder}/tmp/precision-${sampleName}vsHC_union_${type}/comparison.txt" >> "${outputFolder}/precision_output.txt"
+		
 		##HC callset vs sample (sensitivity)
 		# shellcheck disable=SC2154
-		gatk VariantEval \
-		-R "${refGenome}" \
-		-O "${outputFolder}/tmp/sensitivity-HCvs${sampleName}_union.${type}.vcf" \
-		--comp "${outputFolder}/tmp/${sampleName}_${type}.union.20bp_filtered.vcf" \
-		--eval "/apps/data/NIST/${namingConvention}/GIAB_HC.${type}_20bp.vcf"
-
+		"${EBROOTNGSMINUTILS}/bin/vcf-compare-precision-sensitivity.sh" \
+		-1 "/apps/data/NIST/${namingConvention}/GIAB_HC.${type}_20bp.vcf" \
+		-2 "${outputFolder}/tmp/${sampleName}_${type}.union.20bp_filtered.vcf" \
+		-o "${outputFolder}/tmp/sensitivity-HCvs${sampleName}_union_${type}/"
+		
 		if [[ "${firstLine}" == "false" ]]
 		then
-			## print header too
-			head -4 "${outputFolder}/tmp/sensitivity-HCvs${sampleName}_union.${type}.vcf" | tail -1 | awk '{OFS="\t"}{print "measurement","Type",$6,$7,$8,$9,$10,$11,"FinalConcordance"}' > "${outputFolder}/sensitivity_output.txt"
-			firstLine="true"
+			awk '{if(NR==1){print "Measurement\tType\t"$0}}' "${outputFolder}/tmp/sensitivity-HCvs${sampleName}_union_${type}/comparison.txt" > "${outputFolder}/sensitivity_output.txt"
+			firstLine="True"
 		fi
+		awk -v type="${type}" '{if(NR>1){print "sensitivity\t"type"\t"$0}}' "${outputFolder}/tmp/sensitivity-HCvs${sampleName}_union_${type}/comparison.txt" >> "${outputFolder}/sensitivity_output.txt"
 
-		head -5 "${outputFolder}/tmp/sensitivity-HCvs${sampleName}_union.${type}.vcf" | tail -1 | awk -v type="${type}" '{OFS="\t"}{print "sensitivity",type,$6,$7,$8,$9,$10,$11,(($10/$6)*100)}' >> "${outputFolder}/sensitivity_output.txt"
 	done
 }
 
@@ -171,16 +167,12 @@ else
 fi
 	
 ##precision
-echo -e "Measurement\tType\tTP\tFP\tTP/TP+FP"
-echo -e "Measurement\tType\tTP\tFP\tTP/TP+FP" >> "${outputFolder}/output.txt"
+head -1 "${outputFolder}/precision_output.txt" > "${outputFolder}/output.txt"
 
 #awk '{if (NR>1){print $1,$2"\t"$5"\t"$4"\t"$6}}' "${outputFolder}/precision_output.txt"
-awk '{if (NR>1){print $1,$2"\t"$5"\t"($3-$7)"\t"(($7/$3)*100)"\t"}}' "${outputFolder}/precision_output.txt"
-awk '{if (NR>1){print $1,$2"\t"$5"\t"($3-$7)"\t"(($7/$3)*100)"\t"}}' "${outputFolder}/precision_output.txt" >> "${outputFolder}/output.txt"
-
-##sensitivity
-echo -e "Measurement\tType\tTP\tFN\tTP/TP+FN"
-echo -e "Measurement\tType\tTP\tFN\tTP/TP+FN" >> "${outputFolder}/output.txt"
+awk '{if (NR>1){print $0}}' "${outputFolder}/precision_output.txt" >> "${outputFolder}/output.txt"
+cat "${outputFolder}/precision_output.txt" 
+echo -e "\n"  >> "${outputFolder}/output.txt" 
 
-awk '{if (NR>1){print $1,$2"\t"$5"\t"($3-$7)"\t"(($7/$3)*100)"\t"}}' "${outputFolder}/sensitivity_output.txt"
-awk '{if (NR>1){print $1,$2"\t"$5"\t"($3-$7)"\t"(($7/$3)*100)"\t"}}' "${outputFolder}/sensitivity_output.txt" >> "${outputFolder}/output.txt"
+cat "${outputFolder}/sensitivity_output.txt"
+awk '{if (NR>1){print $0}}' "${outputFolder}/sensitivity_output.txt" >> "${outputFolder}/output.txt"
diff --git a/bin/concordanceCheck-ManyToManyVCFs.sh b/bin/concordanceCheck-ManyToManyVCFs.sh
old mode 100644
new mode 100755
diff --git a/bin/convertDos2Unix.sh b/bin/convertDos2Unix.sh
old mode 100644
new mode 100755
diff --git a/bin/countCoverage.sh b/bin/countCoverage.sh
old mode 100644
new mode 100755
diff --git a/bin/create_per_base_intervals.sh b/bin/create_per_base_intervals.sh
old mode 100644
new mode 100755
diff --git a/bin/getNgsFilesDiagnosticsPrmSystem.sh b/bin/getNgsFilesDiagnosticsPrmSystem.sh
old mode 100644
new mode 100755
diff --git a/bin/makeArrayReferenceSamplesheet.sh b/bin/makeArrayReferenceSamplesheet.sh
old mode 100644
new mode 100755
diff --git a/bin/makeFinishedAndEnvFiles.sh b/bin/makeFinishedAndEnvFiles.sh
old mode 100644
new mode 100755
diff --git a/bin/parseManVarList.sh b/bin/parseManVarList.sh
old mode 100644
new mode 100755
diff --git a/bin/revertFromBamToFastQ.sh b/bin/revertFromBamToFastQ.sh
old mode 100644
new mode 100755
diff --git a/bin/runGavin.sh b/bin/runGavin.sh
old mode 100644
new mode 100755
diff --git a/bin/vcf-compare-precision-sensitivity.sh b/bin/vcf-compare-precision-sensitivity.sh
new file mode 100755
index 0000000..0e60738
--- /dev/null
+++ b/bin/vcf-compare-precision-sensitivity.sh
@@ -0,0 +1,257 @@
+#!/usr/bin/env bash
+
+#
+# Bash sanity
+#
+set -e  # Exit if any subcommand or pipeline returns a non-zero status.
+set -u  # Exit if any uninitialised variable is used.
+
+showHelp() {
+		cat <<EOH
+##################################################################################################'
+This tool compares 2 VCF files, based on the variants of vcf1 (or GZIPPED vcf) and shows only the different rows based on the following columns:
+CHROM, POS, REF, ALT and SampleID:GT
+
+Usage:
+bash vcf-compare-precision-sensitivity.sh -1 <input_vcf_file> -2 <input_vcf_file>  -o <output_folder>
+
+Example:
+bash vcf-compare-precision-sensitivity.sh \
+-1 old_analysis.snps.final.vcf \
+-2 new_analysis.snps.final.vcf \
+-o ./results/
+##################################################################################################
+EOH
+trap - EXIT
+exit 0
+}
+
+
+declare VCF1=""
+declare VCF2=""
+declare OUT=""
+#
+# Take the parameters given on the commandline and assign them to variables.
+#
+while getopts ":1:2:d:o:h" opt;
+do
+	case "${opt}" in 1)  VCF1="${OPTARG}";; 2)  VCF2="${OPTARG}";; o)  OUT="${OPTARG}";; h) showHelp ;;
+	esac
+done
+
+#
+# Check if all parameters are set.
+#
+
+
+if [[ -z "${VCF1:-}" ]]
+then
+	echo -e '\nERROR: Must specify a first VCF!\n'
+	showHelp
+	exit 1
+fi
+
+if [[ -z "${VCF2:-}" ]]
+then
+	echo -e '\nERROR: Must specify a second VCF!\n'
+	showHelp
+	exit 1
+fi
+
+if [[ -z "${OUT:-}" ]]
+then
+	echo -e '\nERROR: Must specify an output folder!\n'
+	showHelp
+	exit 1
+fi
+
+#
+# Create tmp folders.
+#
+SCRATCH="${OUT}/TMP/"
+rm -Rf "${SCRATCH}"
+mkdir -p "${SCRATCH}"
+
+printf "vcf1:${VCF1}\nvcf2:${VCF2}"> "${OUT}/runparameters.txt"
+#
+# select filenames from given path and check if they are unique.
+#
+
+checkformatVCF1="${VCF1##*.}"
+checkformatVCF2="${VCF2##*.}"
+
+if [ "${checkformatVCF1}" != "${checkformatVCF2}" ]
+then
+	echo "formats are not the same (${checkformatVCF1} vs ${checkformatVCF2})"
+	exit 1
+fi
+
+if [[ "${checkformatVCF1}" == "gz" ]]
+then
+	inputVcf1="${VCF1%.*}"
+	gzip -c -d "${VCF1}" > "${inputVcf1}"
+
+	inputVcf2="${VCF2%.*}"
+	gzip -c -d "${VCF2}" > "${inputVcf2}"
+elif [[ "${checkformatVCF1}" == 'vcf' ]]
+then
+	inputVcf1="${VCF1}"
+	inputVcf2="${VCF2}"
+else
+	echo 'not a correct format, please use vcf or vcf.gz'
+	exit 1
+fi
+
+vcf01="$(basename ${inputVcf1})"
+vcf02="$(basename ${inputVcf2})"
+if [ "${vcf01}" == "${vcf02}" ]; then
+	echo "files are identical, vcf02 gets a suffix"
+	t="${vcf02}.2"
+	vcf02="${t}"
+fi
+
+##Remove header
+grep -v '^#' "${inputVcf1}" > "${SCRATCH}/${vcf01}.removedHeader.txt"
+## Get only necessary columns
+awk '{OFS="\t"} {print $1,$2,$4,$5,$10}' "${SCRATCH}/${vcf01}.removedHeader.txt" > "${SCRATCH}/${vcf01}.stripColumns_removedHeader.txt"
+##get only genotype call
+awk -F '[\t:]' '{OFS="-"}{print $1,$2,$3,$4,$5}' "${SCRATCH}/${vcf01}.stripColumns_removedHeader.txt" > "${SCRATCH}/${vcf01}.stripped.txt"
+grep -v '0/0' "${SCRATCH}/${vcf01}.stripped.txt" | grep -v "\./\." > "${SCRATCH}/${vcf01}.strippedReferenceCalls.txt"
+
+awk '{OFS="\t"} {print $1,$2,$4,$5,$10}' "${inputVcf2}" > "${SCRATCH}/${vcf02}.stripped.txt"
+grep -v '^#' "${SCRATCH}/${vcf02}.stripped.txt" > "${SCRATCH}/${vcf02}.stripColumns_removedHeader.txt"
+awk -F '[\t:]' '{OFS="-"}{print $1,$2,$3,$4,$5}' "${SCRATCH}/${vcf02}.stripColumns_removedHeader.txt" > "${SCRATCH}/${vcf02}.stripped.txt"
+grep -v '0/0' "${SCRATCH}/${vcf02}.stripped.txt" | grep -v "\./\." > "${SCRATCH}/${vcf02}.strippedReferenceCalls.txt"
+
+
+declare -A arrVCF1
+declare -A arrVCF2
+
+
+while read line 
+do
+	OLDIFS="${IFS}"
+	IFS="-"
+	set ${line}
+	chr="${1}"
+	pos="${2}"
+	ref="${3}"
+	alt="${4}"
+	gen="${5}"
+	IFS="${OLDIFS}"
+	gen="${gen/|//}"
+	myvalue="${ref}-${alt}-${gen}"
+	mykey="${chr}-${pos}"
+	arrVCF1["${mykey}"]="${myvalue}"
+
+done<"${SCRATCH}/${vcf01}.strippedReferenceCalls.txt"
+
+while read line 
+do
+	OLDIFS="${IFS}"
+	IFS="-"
+	set ${line}
+	chr="${1}"
+	pos="${2}"
+	ref="${3}"
+	alt="${4}"
+	gen="${5}"
+	IFS="${OLDIFS}"
+	gen="${gen/|//}"
+	arrVCF2["${chr}-${pos}"]="${ref}-${alt}-${gen}"
+
+done<"${SCRATCH}/${vcf02}.strippedReferenceCalls.txt"
+printf "" > "${SCRATCH}/differences.txt"
+printf "" > "${SCRATCH}/diff.txt"
+
+echo "comparing vcf1 with vcf2"
+for i in "${!arrVCF1[@]}"
+do
+	if [[ "${arrVCF2[$i]+abc}" ]]
+	then
+		if [ "${arrVCF1[$i]}" != "${arrVCF2[$i]}" ]
+		then
+			printf "${i} \t| ${arrVCF1[$i]}\t|\t${arrVCF2[$i]} \n" >> "${SCRATCH}/diff.txt"
+			printf "${i} \t| ${arrVCF1[$i]}\t|\t${arrVCF2[$i]} \n" >> "${SCRATCH}/inconsistent.txt"
+		else
+			printf "${i} ${arrVCF1[$i]}\n" >> "${SCRATCH}/truePos.txt"
+		fi
+	else
+		printf "${i}\t${arrVCF1[$i]}\n" >> "${SCRATCH}/diff.txt"
+		printf "${i}\t${arrVCF1[$i]}\n" >> "${SCRATCH}/notInVcf2.txt"
+	fi
+done
+
+sort -n -k1 "${SCRATCH}/diff.txt" > "${SCRATCH}/differences.txt"
+perl -pi -e 's|-|\t|' "${SCRATCH}/differences.txt"
+printf "" > "${OUT}/vcfStats.txt"
+
+alarm=0
+falseNegative=0
+falsePositive=0
+
+##NOT IN VCF2
+if [[ -f "${SCRATCH}/notInVcf2.txt" ]]
+then
+	falseNegative=$(cat "${SCRATCH}/notInVcf2.txt" | wc -l)
+	sort -V -k1 "${SCRATCH}/notInVcf2.txt" > "${SCRATCH}/notInVcf2.txt.sorted"
+	printf "chr\tpos\tref\talt\tgen\n" > "${OUT}/notInVcf2.txt"
+	cat "${SCRATCH}/notInVcf2.txt.sorted" >> "${OUT}/notInVcf2.txt"
+	perl -pi -e 's|-|\t|g' "${OUT}/notInVcf2.txt"
+fi
+
+## INCONSISTENT
+if [[ -f "${SCRATCH}/inconsistent.txt" ]]
+then
+	alarm=$(cat "${SCRATCH}/inconsistent.txt" | wc -l)
+	sort -V -k1 "${SCRATCH}/inconsistent.txt" > "${SCRATCH}/inconsistent.txt.sorted"
+	printf "\t\t\t|\tvcf1\t\t|\t\tvcf2\t\t\n" > "${OUT}/inconsistent.txt"
+	printf "chr\tposition\t| ref\talt\tgen\t|\tref\talt\tgen\n" >> "${OUT}/inconsistent.txt"
+	cat "${SCRATCH}/inconsistent.txt.sorted" >> "${OUT}/inconsistent.txt"
+	perl -pi -e 's|-|\t|g' "${OUT}/inconsistent.txt"
+	
+fi
+
+##TRUE POS
+truePos=$(cat "${SCRATCH}/truePos.txt" | wc -l)
+sort -V -k1 "${SCRATCH}/truePos.txt" > "${SCRATCH}/truePos.txt.sorted"
+printf "chr\tpos\tref\talt\tgen\n" > "${OUT}/truePos.txt"
+cat "${SCRATCH}/truePos.txt.sorted" >> "${OUT}/truePos.txt"
+
+perl -pi -e 's|-|\t|g' "${OUT}/truePos.txt"
+
+
+total=$((truePos + alarm + falseNegative))
+printf "TotalNumber:${total}\n" >> "${OUT}/vcfStats.txt"
+##TRUE POS
+tpr=$(awk "BEGIN {printf \"%.2f\n\", ((${truePos}/$total)*100)}")
+printf "TP:$truePos, TP rate: ${tpr}%%\n" >> "${OUT}/vcfStats.txt"
+
+if [[ "${falseNegative}" -ne 0 ]]
+then
+	fnr=$(awk "BEGIN {printf \"%.2f\n\", ((${falseNegative}/$total)*100)}")
+	printf "FN:${falseNegative}, FN rate: ${fnr}%%\n" >> "${OUT}/vcfStats.txt"	
+else
+	printf "FP:${falseNegative}, FN rate: 0%%\n" >> "${OUT}/vcfStats.txt"
+
+fi
+if [[ "${alarm}" -ne 0 ]]
+then
+	alarmRate=$(awk "BEGIN {printf \"%.2f\n\", ((${alarm}/$total)*100)}")
+	printf "Inconsistent:${alarm}, InconsistentRate: ${alarmRate}%%\n" >> "${OUT}/vcfStats.txt"
+else
+	printf "Inconsistent:${alarm}, InconsistentRate: 0%%\n" >> "${OUT}/vcfStats.txt"
+fi
+
+totalDifferences=$((${falseNegative}+${alarm}))
+
+printf "${total}\t${truePos}\t${totalDifferences}" > "${OUT}/simpleStats.txt"
+
+
+concordant=$(awk '{print 100-(($3/$1)*100)}' "${OUT}/simpleStats.txt")
+printf "Total\tTP\tdiff\tconcordant(100-((diff/total)*100)\n" > "${OUT}/comparison.txt"
+printf "${total}\t${truePos}\t${totalDifferences}\t${concordant}\n" >> "${OUT}/comparison.txt"
+
+printf "done..\nComparison can be found: ${OUT} \n"
+
+exit 0