Hg19 and hg38 analysis from same workflow branch

README.md

@@ -131,6 +131,17 @@ The optional configuration JSON file defaults to the `convertToStdVCF.json` resi
 
 ## Changelog
 
+* 3.0.0
+  * Major
+    * Support for hg38/GRCh38 reference genome and variant calling from ALT and HLA contigs.
+  * Minor
+    * For hg38: Removing mappability and repeat elements' annotations from penalty calculations.
+    * skipREMAP: Option to remove repeat elements and mappability from confidence annotations in hg19.
+    * Removing EVS And ExAC AF from the annotations and no-control workflow filtering
+    * Support for variant calling from CRAM files
+    * Bug fix: Removing "quote" around the raw filter option `<RAW_SNV_FILTER_OPTIONS>`
+    * Update `COWorkflowsBasePlugin` to `1.4.2`
+
 * 2.2.0
 
   * minor: Added `vcfConvertToStd.py`; slightly modified from code by @juleskers and Sophia Stahl

buildinfo.txt

@@ -1,4 +1,4 @@
-dependson=COWorkflowsBasePlugin:1.3.0
+dependson=COWorkflowsBasePlugin:1.4.2
 JDKVersion=1.8
 GroovyVersion=2.4
 RoddyAPIVersion=3.4

buildversion.txt

@@ -1,2 +1,2 @@
-2.1
+3.0
 0

resources/analysisTools/snvPipeline/PurityReloaded.py

@@ -251,6 +251,10 @@ def parseVcf(file,num):
 	while (l!= ""):
 		t=l.split('\t')
 		if (t[0][0] != "#") and isValid(t):
+			# Skiping the non-primary assembly variants from purity calculations
+			if t[0].startswith('HLA') or t[0].endswith('_alt'):
+				l=vcf.readline()
+				continue
 			i = chromMap[t[0]]
 			if (t[12]=="germline"):
 			  #DP5=string.split(string.split(t[11],";")[1],",")

resources/analysisTools/snvPipeline/createErrorPlots.py

@@ -31,7 +31,7 @@ def calculateLogSize(size, max_val, base):
 	return math.log(((size/max_val)*(base-1.))+1., base)
 
 def calculateRootedSize(size, max_val):
-	if(float(size) != 0.0):
+	if(float(size) != 0.0 and float(max_val) != 0.0):
 		return np.sqrt(size/max_val)
 	else:
 		return 0.0
@@ -199,6 +199,10 @@ def calculateErrorMatrix(vcfFilename, referenceFilename, errorType):
 			# 23.05.2016 JB: Excluded multiallelic SNVs
 			if ',' in split_line[header.index("ALT")]: continue
 
+			# 21.02.2023 NP: Excluded SNVs with 'N' before or after "," in context
+			if 'N,' in split_line[header.index("SEQUENCE_CONTEXT")] or ',N' in split_line[header.index("SEQUENCE_CONTEXT")]:
+				continue
+
 			chrom = split_line[header.index("CHROM")]
 			pos = int(split_line[header.index("POS")])
 			context = "" 

resources/analysisTools/snvPipeline/environments/tbi-lsf-cluster.sh

@@ -19,7 +19,7 @@ module load bedtools/"${BEDTOOLS_VERSION:?BEDTOOLS_VERSION undefined}"
 module load pypy/"${PYPY_VERSION:?PYPY_VERSION undefined}"
 
 set +ue
-source /dkfz/cluster/virtualenvs/paramasi/python_2.7.9_SNVCalling_pysam_0.16.0.1/bin/activate
+source /omics/groups/OE0246/shared/paramasi/compute_env/python_2.7.9_SNVCalling_pysam_0.16.0.1/bin/activate
 set -ue
 
 export BGZIP_BINARY=bgzip

resources/analysisTools/snvPipeline/filter_vcf.sh

@@ -24,7 +24,7 @@ getRefGenomeAndChrPrefixFromHeader ${TUMOR_BAMFILE_FULLPATH_BP} # Sets CHR_PREFI
 ALIGNMENT_FOLDER=`dirname ${TUMOR_BAMFILE_FULLPATH_BP}`
 
 # bugfix: ensure to interpret CHROMOSOME_INDICES as array - otherwise TOOL_INTERMUTATION_DISTANCE_COORD_COLOR will fail...
-declare -a CHROMOSOME_INDICES="${CHROMOSOME_INDICES}"
+declare -a CHROMOSOME_INDICES="${CHROMOSOME_INDICES_PLOTTING}"
 numberOfChromosomes=${CHROMOSOME_INDICES[@]}
 outputFilenamePrefix=${mpileupDirectory}/${SNVFILE_PREFIX}${PID}
 outputFilenamePrefix_original=${outputFilenamePrefix}

resources/analysisTools/snvPipeline/in_dbSNPcounter.pl

@@ -23,7 +23,7 @@
 {
 	$minscore = 8;
 }
-open (FH, $file) or die "Could not open $file: $!\n";
+open (my $FH, $file) or die "Could not open $file: $!\n";
 
 # count all, somatic, s. with minconfidence, in dbSNP, in 1KG
 my $all = 0;
@@ -37,85 +37,80 @@
 
 
 my $header = "";
-while ($header = <FH>)
-{
-	last if ($header =~ /^\#CHROM/); # that is the line with the column names
-}
-chomp $header;
-
-my $DBSBP = 13;
-my $KG = 14;
-my $CONFIDENCE = 28;
-my $CANNOTATION = -1;
-my $RECLASSIFICATION = -1;
-my $CLASSIFICATION;
+my ($DBSBP, $KG, $CONFIDENCE, $CLASSIFICATION);
 
-@help = split(/\t/, $header);
-for (my $c = 0; $c < @help; $c++)
-{
-	# fixed column labels (from vcf_pileup_compare)
-	if ($help[$c] eq "CONFIDENCE")
-	{
-		$CONFIDENCE = $c;
-		print STDERR "CONFIDENCE in column $c\n";
-	}
-	if ($help[$c] eq "1K_GENOMES")
+while(!eof($FH)){
+	my $line = readline($FH) || die "Could not read line: $?";
+	chomp $line;
+	if ($line =~ /^#/)
 	{
-		$KG = $c;
-		print STDERR "INFO in column $c\n";
-	}
-	if ($help[$c] eq "DBSNP")
-	{
-		$DBSBP = $c;
-		print STDERR "DBSNP_COL in column $c\n";
-	}
-	if ($help[$c] eq "ANNOTATION_control")
-    {
-    	$CANNOTATION = $c;
-    	print STDERR "ANNOTATION_control in column $c\n";
-    }
-    if ($help[$c] eq "RECLASSIFICATION")
-    {
-        $RECLASSIFICATION = $c;
-        print STDERR "RECLASSIFICATION in column $c\n";
-    }
-}
+		#print STDOUT "HELLO\n";
+		if ($line =~/^#CHROM/){
+			chomp $line;
 
-if ($CANNOTATION > 0) {
-    $CLASSIFICATION = $CANNOTATION;
-} else {
-    $CLASSIFICATION = $RECLASSIFICATION;
-}
+			my @head=split("\t", $line);
+			my %col;
 
-# I know that it's evilly hardcoded!
-while (<FH>)
-{
-	if ($_ =~ /^#/)	# skip header lines
-	{
-		next;
-	}
-	$all++;
-	@help = split ("\t", $_);
-	if ($help[$CLASSIFICATION] =~ /somatic/)
-	{
-		$somatic++;
-		if ($help[$CONFIDENCE] >= $minscore)
-		{
-			$scored++;
-			#print STDERR $_;
-			if ($help[$DBSBP] =~ /MATCH=exact/)
+			my $i = 0;
+			while($i < @head)
 			{
-				$dbSNP++;
+				if($head[$i] eq "DBSNP"){
+					$col{"DBSNP"} = $i;
+					print STDERR "DBSNP in column ", $i+1,"\n";
+				}
+				if($head[$i] eq "1K_GENOMES"){
+					$col{"1K_GENOMES"} = $i;
+					print STDERR "1K_GENOMES in column ", $i+1,"\n";
+				}
+				if($head[$i] eq "RECLASSIFICATION"){
+					$col{"RECLASSIFICATION"} = $i;
+					print STDERR "RECLASSIFICATION in column ", $i+1,"\n";
+				}
+				if($head[$i] eq "ANNOTATION_control"){
+					$col{"ANNOTATION_control"} = $i;
+					print STDERR "ANNOTATION_control in column ", $i+1,"\n";
+				}
+				if($head[$i] eq "CONFIDENCE"){
+					$col{"CONFIDENCE"} = $i;
+					print STDERR "CONFIDENCE in column ", $i+1,"\n";
+				}
+				$i++;
 			}
-			if ($help[$KG] =~ /MATCH=exact/)
+
+			$DBSBP = $col{"DBSNP"};
+			$KG = $col{"1K_GENOMES"};
+			$CONFIDENCE = $col{"CONFIDENCE"};
+
+			if ($col{"ANNOTATION_control"} > 0) {
+				$CLASSIFICATION = $col{"ANNOTATION_control"};
+			} else {
+				$CLASSIFICATION = $col{"RECLASSIFICATION"};
+			}
+		}
+	}
+	else{
+		$all++;
+		@help = split ("\t", $line);
+		if ($help[$CLASSIFICATION] =~ /somatic/)
+		{
+			$somatic++;
+			if ($help[$CONFIDENCE] >= $minscore)
 			{
-				$oneKG++;
+				$scored++;
+				if ($help[$DBSBP] =~ /MATCH=exact/)
+				{
+					$dbSNP++;
+				}
+				if ($help[$KG] =~ /MATCH=exact/)
+				{
+					$oneKG++;
+				}
 			}
 		}
 	}
 }
+close $FH;
 
-close FH;
 if ($scored > 0)
 {
 	$perc_dbSNP = sprintf ("%.2f", ($dbSNP/$scored*100));
@@ -126,6 +121,5 @@
 else	# there might be no ...
 {
 	die "!!! There are no SNVs with confidence >= $minscore in the input, it makes no sense to do further analyses with the current settings on these data!!!\n";
-
 }
 exit;

resources/analysisTools/snvPipeline/intermutationDistance_Coord_color.r

@@ -45,6 +45,14 @@ c.array <- unlist(strsplit(opt$chrArray, ',', fixed = TRUE))
 data <- read.table(opt$chrLengthFile, header=FALSE)
 chrLength <- data.frame(data)
 rownames(chrLength) <- chrLength$V1
+
+if(opt$chrPrefix != "" && 
+  grepl(opt$chrPrefix, chrLength$V1[1]) && 
+	!grepl(opt$chrPrefix, c.array[1])){
+
+    c.array <- paste0(opt$chrPrefix, c.array, opt$chrSuffix)
+}
+
 xtotal <- sum(chrLength[c.array,2]/10)
 xoffsets <- c(0)
 
@@ -84,7 +92,7 @@ pdf(opt$outFilePrefix, width=20, height=8)
 plotColors = c("CA"="blue","CG"="black","CT"="red","TA"="purple","TC"="orange","TG"="green")
 baseChanges <- c("CA", "CG", "CT", "TA", "TC","TG")
 
-c.name <- paste0(opt$chrPrefix, c.array[1], opt$chrSuffix)  
+c.name <- c.array[1]
 
 sel <- which(dat$diff > 0)
 if(length(sel)){
@@ -101,7 +109,7 @@ if(length(sel)){
 	# chromosomes <- c(2:22, 'X')
 
 	for (chr in c.array) {
-	  c.name <- paste0(opt$chrPrefix, chr, opt$chrSuffix)  
+	  c.name <- chr
 
 	  sel <- which(dat$X.CHROM == c.name & dat$diff > 0)
 	  points((dat$POS[sel]/10+xoffset)/xtotal, log10(dat$diff[sel]), col = plotColors[dat$change[sel]], pch=16,cex=0.8)

resources/analysisTools/snvPipeline/snvAnnotation.sh

@@ -17,7 +17,7 @@ declare -r outputDirectory=`dirname ${FILENAME_VCF_OUT}`
 relinked=false
 # (Re-)link bam file and index. The pipeline cannot handle i.e. .mdup.bam and .mdup.bai
 # Look up the index with .bam.bai. If the file exists nothing happens.
-if [[ ! -f ${TUMOR_BAMFILE_FULLPATH_BP}.bai ]]
+if [[ ! -f ${TUMOR_BAMFILE_FULLPATH_BP}.bai && ! -f ${TUMOR_BAMFILE_FULLPATH_BP}.crai ]]
 then
     shortBamIdx=`dirname ${TUMOR_BAMFILE_FULLPATH_BP}`"/"`basename ${TUMOR_BAMFILE_FULLPATH_BP} .bam`".bai"
     [[ ! -f ${shortBamIdx} ]] && echo "Bam index file cannot be found!" && exit -15
@@ -91,12 +91,10 @@ fi
 
 cmdFilter="${cmdFilter} | ${PERL_BINARY} ${TOOL_ANNOTATE_VCF_FILE} --tabix_bin=${TABIX_BINARY} -a - -b ${DBSNP} --columnName=${DBSNP_COL} --reportMatchType  --bAdditionalColumn=2 --reportLevel 4 | \
     ${PERL_BINARY} ${TOOL_ANNOTATE_VCF_FILE} --tabix_bin=${TABIX_BINARY} -a - -b ${KGENOME} --columnName=${KGENOMES_COL}  --reportMatchType --bAdditionalColumn=2 --reportLevel 4 | \
-    ${PERL_BINARY} ${TOOL_ANNOTATE_VCF_FILE} --tabix_bin=${TABIX_BINARY} -a - -b ${ExAC} --columnName ${ExAC_COL} --bFileType vcf --reportMatchType --reportLevel 4 | \
-    ${PERL_BINARY} ${TOOL_ANNOTATE_VCF_FILE} --tabix_bin=${TABIX_BINARY} -a - -b ${EVS} --columnName ${EVS_COL} --bFileType vcf --reportMatchType --reportLevel 4 | \
-    ${PERL_BINARY} ${TOOL_ANNOTATE_VCF_FILE} -a - -b ${GNOMAD_WES_ALL_SNV} --columnName=${GNOMAD_WES_COL} --bFileType vcf --reportMatchType --reportLevel 4 | \
-    ${PERL_BINARY} ${TOOL_ANNOTATE_VCF_FILE} -a - -b ${GNOMAD_WGS_ALL_SNV} --columnName=${GNOMAD_WGS_COL} --bFileType vcf --reportMatchType --reportLevel 4 | \
+    ${PERL_BINARY} ${TOOL_ANNOTATE_VCF_FILE} --tabix_bin=${TABIX_BINARY} -a - -b ${GNOMAD_WES_ALL_SNV} --columnName=${GNOMAD_WES_COL} --bFileType vcf --reportMatchType --reportLevel 4 | \
+    ${PERL_BINARY} ${TOOL_ANNOTATE_VCF_FILE} --tabix_bin=${TABIX_BINARY} -a - -b ${GNOMAD_WGS_ALL_SNV} --columnName=${GNOMAD_WGS_COL} --bFileType vcf --reportMatchType --reportLevel 4 | \
     ${PERL_BINARY} ${TOOL_ANNOTATE_VCF_FILE} --tabix_bin=${TABIX_BINARY} -a - -b ${LOCALCONTROL_WGS} --columnName ${LOCALCONTROL_WGS_COL} --bFileType vcf --reportMatchType --reportLevel 4 | \
-    ${PERL_BINARY} ${TOOL_ANNOTATE_VCF_FILE} --tabix_bin=${TABIX_BINARY} -a - -b ${LOCALCONTROL_WES} --columnName ${LOCALCONTROL_WES_COL} --bFileType vcf --reportMatchType --reportLevel 4"
+    ${PERL_BINARY} ${TOOL_ANNOTATE_VCF_FILE} --tabix_bin=${TABIX_BINARY} -a - -b ${LOCALCONTROL_WES} --columnName ${LOCALCONTROL_WES_COL} --bFileType vcf --reportMatchType --reportLevel 4 "
 
 if [[ -f ${RECURRENCE} ]]; then
     cmdFilter="${cmdFilter} | ${PERL_BINARY} ${TOOL_ANNOTATE_VCF_FILE} -a - -b ${RECURRENCE} --columnName ${RECURRENCE_COL} --bFileType vcf"
@@ -199,7 +197,8 @@ mkfifo ${npConfidence}
 if [[ ${isNoControlWorkflow-false} == "false" ]]; then
     cat ${filenameSNVVCF} > ${npConfidence} &
 else
-    cat ${filenameSNVVCF} | ${PYPY_OR_PYTHON_BINARY} -u ${TOOL_CONFIDENCE_ANNOTATION} ${noControlFlag} -i - ${CONFIDENCE_OPTS} -a 0 > ${npConfidence} &
+    cat ${filenameSNVVCF} | ${PYPY_OR_PYTHON_BINARY} -u ${TOOL_CONFIDENCE_ANNOTATION} ${noControlFlag} -i - ${CONFIDENCE_OPTS} -a 0 \
+        --gnomAD_WGS_maxMAF=${CRIT_GNOMAD_GENOMES_maxMAF} --gnomAD_WES_maxMAF=${CRIT_GNOMAD_EXOMES_maxMAF} --localControl_WGS_maxMAF=${CRIT_LOCALCONTROL_maxMAF} --localControl_WES_maxMAF=${CRIT_LOCALCONTROL_maxMAF} --1000genome_maxMAF=${CRIT_1KGENOMES_maxMAF} > ${npConfidence} &
 fi
 
 # create BaseScore FIFOs and their consumer processes (zip and write to target file)
@@ -214,7 +213,8 @@ cat ${filenameReferenceAlleleReadPositions}_NP | ${BGZIP_BINARY} -f >${filenameR
 if [[ ${runArtifactFilter-true} == true ]]
 then
 	cat ${npConfidence} | filterPeOverlap ${noControlFlag} --alignmentFile=${tumorbamfullpath} --mapq=$mapqual --baseq=$basequal --qualityScore=phred --maxNumberOfMismatchesInRead=${NUMBER_OF_MISMACTHES_THRESHOLD--1} --altBaseQualFile=${filenameAlternativeAlleleBaseScores}_NP --refBaseQualFile=${filenameReferenceAlleleBaseScores}_NP --altBasePositionsFile=${filenameAlternativeAlleleReadPositions}_NP --refBasePositionsFile ${filenameReferenceAlleleReadPositions}_NP --referenceFile=${REFERENCE_GENOME} \
-						| ${PYPY_OR_PYTHON_BINARY} -u ${TOOL_CONFIDENCE_ANNOTATION} ${noControlFlag} -i - ${CONFIDENCE_OPTS} -a 0 -f ${filenameSomaticSNVsTmp} > ${filenameSNVVCFTemp}.tmp
+						| ${PYPY_OR_PYTHON_BINARY} -u ${TOOL_CONFIDENCE_ANNOTATION} ${noControlFlag} -i - ${CONFIDENCE_OPTS} -a 0 -f ${filenameSomaticSNVsTmp} \
+                            --gnomAD_WGS_maxMAF=${CRIT_GNOMAD_GENOMES_maxMAF} --gnomAD_WES_maxMAF=${CRIT_GNOMAD_EXOMES_maxMAF} --localControl_WGS_maxMAF=${CRIT_LOCALCONTROL_maxMAF} --localControl_WES_maxMAF=${CRIT_LOCALCONTROL_maxMAF} --1000genome_maxMAF=${CRIT_1KGENOMES_maxMAF} > ${filenameSNVVCFTemp}.tmp
 
     [[ $? != 0 ]] && echo "Error in first iteration of confidence annotation" && exit 2
 
@@ -243,7 +243,8 @@ then
     fi
 
 	cat ${filenameSNVVCFTemp} | ${PYTHON_BINARY} ${TOOL_FLAG_BIAS} --vcfFile="/dev/stdin" --referenceFile=${REFERENCE_GENOME} --sequence_specificFile=${filenamePCRerrorMatrix} --sequencing_specificFile=${filenameSequencingErrorMatrix} --numReads=${nReads} --numMuts=${nMuts} --biasPValThreshold=${biasPValThreshold} --biasRatioThreshold=${biasRatioThreshold} --biasRatioMinimum=${biasRatioMinimum} --maxNumOppositeReadsSequencingWeakBias=${maxNumOppositeReadsSequencingWeakBias} --maxNumOppositeReadsSequenceWeakBias=${maxNumOppositeReadsSequenceWeakBias} --maxNumOppositeReadsSequencingStrongBias=${maxNumOppositeReadsSequencingStrongBias} --maxNumOppositeReadsSequenceStrongBias=${maxNumOppositeReadsSequenceStrongBias} --ratioVcf=${rVcf} --bias_matrixSeqFile=${filenameBiasMatrixSeqFile} --bias_matrixSeqingFile=${filenameBiasMatrixSeqingFile} --vcfFileFlagged="/dev/stdout" | \
-	${PYPY_OR_PYTHON_BINARY} -u ${TOOL_CONFIDENCE_ANNOTATION} ${noControlFlag} -i - ${CONFIDENCE_OPTS} -a 1 -f ${filenameSomaticSNVsTmp} > ${filenameSNVVCFTemp}.tmp
+	${PYPY_OR_PYTHON_BINARY} -u ${TOOL_CONFIDENCE_ANNOTATION} ${noControlFlag} -i - ${CONFIDENCE_OPTS} -a 1 -f ${filenameSomaticSNVsTmp} \
+        --gnomAD_WGS_maxMAF=${CRIT_GNOMAD_GENOMES_maxMAF} --gnomAD_WES_maxMAF=${CRIT_GNOMAD_EXOMES_maxMAF} --localControl_WGS_maxMAF=${CRIT_LOCALCONTROL_maxMAF} --localControl_WES_maxMAF=${CRIT_LOCALCONTROL_maxMAF} --1000genome_maxMAF=${CRIT_1KGENOMES_maxMAF} > ${filenameSNVVCFTemp}.tmp
 
 	[[ $? != 0 ]] && echo "Error in first filtering and/or second interation of confidence annotation" && exit 5
 
@@ -267,7 +268,8 @@ then
     fi
 
 	cat ${filenameSNVVCFTemp} | ${PYTHON_BINARY} -u ${TOOL_FLAG_BIAS} --vcfFile="/dev/stdin" --referenceFile=${REFERENCE_GENOME} --sequence_specificFile=${filenamePCRerrorMatrix} --sequencing_specificFile=${filenameSequencingErrorMatrix} --numReads=${nReads} --numMuts=${nMuts} --biasPValThreshold=${biasPValThreshold} --biasRatioThreshold=${biasRatioThreshold} --biasRatioMinimum=${biasRatioMinimum} --maxNumOppositeReadsSequencingWeakBias=${maxNumOppositeReadsSequencingWeakBias} --maxNumOppositeReadsSequenceWeakBias=${maxNumOppositeReadsSequenceWeakBias} --maxNumOppositeReadsSequencingStrongBias=${maxNumOppositeReadsSequencingStrongBias} --maxNumOppositeReadsSequenceStrongBias=${maxNumOppositeReadsSequenceStrongBias} --ratioVcf=${rVcf} --bias_matrixSeqFile=${filenameBiasMatrixSeqFile} --bias_matrixSeqingFile=${filenameBiasMatrixSeqingFile} --vcfFileFlagged="/dev/stdout" | \
-	${PYPY_OR_PYTHON_BINARY} -u ${TOOL_CONFIDENCE_ANNOTATION} ${noControlFlag} -i - ${CONFIDENCE_OPTS_PANCAN} -a 2  > ${filenameSNVVCF}
+	${PYPY_OR_PYTHON_BINARY} -u ${TOOL_CONFIDENCE_ANNOTATION} ${noControlFlag} -i - ${CONFIDENCE_OPTS_PANCAN} -a 2 \
+    --gnomAD_WGS_maxMAF=${CRIT_GNOMAD_GENOMES_maxMAF} --gnomAD_WES_maxMAF=${CRIT_GNOMAD_EXOMES_maxMAF} --localControl_WGS_maxMAF=${CRIT_LOCALCONTROL_maxMAF} --localControl_WES_maxMAF=${CRIT_LOCALCONTROL_maxMAF} --1000genome_maxMAF=${CRIT_1KGENOMES_maxMAF} > ${filenameSNVVCF}
 
 	[[ $? != 0 ]] && echo "Error in second filtering and/or third iteration of confidence annotation" && exit 8
 
@@ -289,7 +291,8 @@ then
 	fi
 else
 	cat ${npConfidence} | filterPeOverlap ${noControlFlag} --alignmentFile=${tumorbamfullpath} --mapq=$mapqual --baseq=$basequal --qualityScore=phred --maxNumberOfMismatchesInRead=${NUMBER_OF_MISMACTHES_THRESHOLD--1} --altBaseQualFile=${filenameAlternativeAlleleBaseScores}_NP --refBaseQualFile=${filenameReferenceAlleleBaseScores}_NP --altBasePositionsFile=${filenameAlternativeAlleleReadPositions}_NP --refBasePositionsFile=${filenameReferenceAlleleReadPositions}_NP --referenceFile=${REFERENCE_GENOME} | \
-	${PYPY_OR_PYTHON_BINARY} -u ${TOOL_CONFIDENCE_ANNOTATION} ${noControlFlag} -i - ${CONFIDENCE_OPTS_PANCAN} > ${filenameSNVVCFTemp}
+	${PYPY_OR_PYTHON_BINARY} -u ${TOOL_CONFIDENCE_ANNOTATION} ${noControlFlag} -i - ${CONFIDENCE_OPTS_PANCAN} \
+    --gnomAD_WGS_maxMAF=${CRIT_GNOMAD_GENOMES_maxMAF} --gnomAD_WES_maxMAF=${CRIT_GNOMAD_EXOMES_maxMAF} --localControl_WGS_maxMAF=${CRIT_LOCALCONTROL_maxMAF} --localControl_WES_maxMAF=${CRIT_LOCALCONTROL_maxMAF} --1000genome_maxMAF=${CRIT_1KGENOMES_maxMAF} > ${filenameSNVVCFTemp}
 
     exitCode=$?
     [[ $exitCode == 0 ]] && [[ -f ${filenameSNVVCFTemp} ]] && mv ${filenameSNVVCFTemp} ${filenameSNVVCF}