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shutil, time -from optparse import OptionParser - - -class VCFCartoWrapper(object): - - def __init__(self): - self._options = None - - - def stop_err(self, msg ): - sys.stderr.write( "%s\n" % msg ) - sys.exit() - - - def setAttributesFromCmdLine(self): - description = "VCFcarto can convert your tabulated file into a file with only the SNP from refA and refH.\n" - description += "2 formats are possible, either the input format is conserved, or the format is changed into a 3 letter format\n" - description += "(\"A\" for refA, \"H\" for refH and \"-\" when the base do not correspond to any parent)\n\n" - description += "example 1 : VCFcarto.py -f Storage.out -A G15 -H G23 -o FilteredStorage.out\n" - description += "example 2 : VCFcarto.py -f Storage.out -A ref1 -H ref2 -p -s -g -m -o cartoTable.out\n" - parser = OptionParser(description = description, version = "0.1") - parser.add_option("-f", "--file", dest = "tableName", action = "store", type = "string", help = "Input TSV File name [compulsory] [format: TSV]", default = "") - parser.add_option("-o", "--output", dest = "outFile", action = "store", type = "string", help = "output TSV File name [compulsory] [format: TSV]", default = "") - parser.add_option("-A", "--refA", dest = "refA", action = "store", type = "string", help = "name of the reference genome A [compulsory] ", default = "") - parser.add_option("-H", "--refH", dest = "refH", action = "store", type = "string", help = "name of the reference genome H [compulsory] ", default = "") - parser.add_option("-p", "--onlyParents", dest = "onlyPar", action = "store_true", help = "Will change every letters by either A or H depending on which parents the strain correspond to for that base[optional] [default: False]", default = False) - parser.add_option("-m", "--mergeMarkers", dest = "mergeMarkers", action = "store_true", help = "Will merge sequential markers with the same information ; option -p is needed [optional] [default: False]", default = False) - parser.add_option("-M", "--mergeFile", dest = "mergeFile", action = "store", type = "string", help = "name for the mergeFile ", default = "") - parser.add_option("-g", "--graphics", dest = "graphs", action = "store_true", help = "create graphs. Only works with -p[optional] [default: False]", default = False) - parser.add_option("-G", "--graphHTML", dest = "graphHTML", action = "store", type = "string", help = "name of the HTML linking to graphs ", default = "") - parser.add_option("-d", "--dirGraphs", dest = "dirGraphs", action = "store", type = "string", help = "name of the folder containing graphs ", default = "") - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - - def _setAttributesFromOptions(self, options): - self._options = options - - def run(self): - prg = "VCFCarto.py" - args = "" - args += "-f %s" % self._options.tableName - args += " " - args += "-o %s" % self._options.outFile - args += " " - args += "-A %s" % self._options.refA - args += " " - args += "-H %s" % self._options.refH - args += " " - args += "-v 2 " - if self._options.onlyPar : - args += " " - args += "-p" - if self._options.mergeMarkers : - args += " " - args += "-m" - if self._options.graphs : - args += " " - args += "-g" - cmd = "%s %s" %(prg, args) - - print cmd - - try: - tmp_err = tempfile.NamedTemporaryFile().name - tmp_stderr = open( tmp_err, 'wb' ) - proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stderr=tmp_stderr ) - returncode = proc.wait() - tmp_stderr.close() - # get stderr, allowing for case where it's very large - tmp_stderr = open( tmp_err, 'rb' ) - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() - if stderr: - raise Exception, stderr - except Exception, e: - self.stop_err( 'Error in VCFCarto:\n' + str( e ) ) - - if self._options.mergeMarkers : - shutil.move("markerList.bed" ,self._options.mergeFile) - if self._options.graphs : - html = open(self._options.graphHTML, "w") - - os.mkdir(self._options.dirGraphs) - lGraphsFiles = glob.glob("VCFCarto_graphs/*") - for file in lGraphsFiles : - baseName = os.path.basename(file) - shutil.move( file ,"%s/%s" %(self._options.dirGraphs, baseName)) - line = " \n" %(baseName) - html.write(line) - -if __name__ == "__main__": - iWrapper = VCFCartoWrapper() - iWrapper.setAttributesFromCmdLine() - iWrapper.run() diff -r a6b557df86db -r 3ca0f78f1102 VCFCarto_wrapper.xml --- a/VCFCarto_wrapper.xml Tue Dec 15 05:35:36 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,315 +0,0 @@ - - VCFcarto can convert a tabulated marker file into a file with only the markers from 2 parents - - VCF_Gandalf_Tools - - - VCFCarto.py --version - - - VCFCarto_wrapper.py -f $inputTabular -o $outputVCFCarto -A $parentA -H $parentH - #if str($outputType) == "carto" - -p -g --graphHTML $output_html --dirGraphs "$output_html.files_path" - #end if - #if str($outputType) == "MergedCarto" - -p -g --graphHTML $output_html --dirGraphs "$output_html.files_path" -m --mergeFile $output_bed - #end if - - - - - - - - - - - - - - - not outputType == "raw" - - - outputType == "MergedCarto" - - - - - - - - - - - - - - - - - - - - - - diff -r a6b557df86db -r 3ca0f78f1102 VCFFiltering_wrapper.py --- a/VCFFiltering_wrapper.py Tue Dec 15 05:35:36 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,110 +0,0 @@ -#!/usr/bin/env python - - -import subprocess, tempfile, sys, os, glob, shutil, time -from optparse import OptionParser -from optparse import Option, OptionValueError - -class VCFFilteringWrapper(object): - - def __init__(self): - self._options = None - - - def stop_err(self, msg ): - sys.stderr.write( "%s\n" % msg ) - sys.exit() - - - def setAttributesFromCmdLine(self): - description = "VCFFiltering_wrapper" - description += "\nWrapper for VCFFiltering ;\n VCFFiltering filters SNP on a VCF depending on depth (DP) allele number (AN), allele frequency (AF) and SNP quality.\n" - description += "example 1 : VCFFiltering.py -f myVCF.vcf -o FilteredVCF.vcf\n" - description += "example 2 : VCFFiltering.py -f myVCF.vcf -N 2 -F 0.87 -b bed1.bed bed2.bed -o FilteredVCF.vcf\n" - parser = OptionParser(description = description, version = "0.1") - parser.add_option("-f", "--vcf", dest = "VCFFile", action = "store", type = "string", help = "Input VCF File name [compulsory] [format: VCF]", default = "") - parser.add_option("-o", "--output", dest = "outFile", action = "store", type = "string", help = "output VCF File name [compulsory] [format: VCF]", default = "") - parser.add_option("-m", "--minDP", dest = "minDP", action = "store", type = "int", help = "minimum of depth ; if both minDP and maxDP are set, optimal DP will not be calculated ", default = 0) - parser.add_option("-M", "--maxDP", dest = "maxDP", action = "store", type = "int", help = "maximum of depth ; if both minDP and maxDP are set, optimal DP will not be calculated ", default = 0) - parser.add_option("-N", "--AN", dest = "AN", action = "store", type = "int", help = "maximum number of allele for a SNP; default = 2", default = 2) - parser.add_option("-F", "--AF", dest = "AF", action = "store", type = "float", help = "minimum frequency for the alternative allele of a SNP; default = 0.9", default = 0.9) - parser.add_option("-b", "--bed", dest = "bedFiles", action = "append", type = "string", help = "bed files: list of coordinates to filter, multiple arguments allowed '-b file1 file2' ", default = []) - parser.add_option("-G", "--graphHTML", dest = "graphHTML", action = "store", type = "string", help = "name of the HTML linking to graphs ", default = "") - parser.add_option("-d", "--dirGraphs", dest = "dirGraphs", action = "store", type = "string", help = "name of the folder containing graphs ", default = "") - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - - def _setAttributesFromOptions(self, options): - self._options = options - - def run(self): - if self._options.minDP and self._options.maxDP : - if self._options.minDP > self._options.maxDP : - self.stop_err( 'error in options : minDP > max DP (%s > %s)' %(self._options.minDP,self._options.maxDP)) - - prg = "VCFFiltering.py -g -G 'png' " - args = "" - args += "-f %s" % self._options.VCFFile - args += " " - args += "-o %s" % self._options.outFile - if self._options.AF : - args += " " - args += "-F %s" % self._options.AF - if self._options.AN : - args += " " - args += "-N %s" % self._options.AN - if self._options.minDP : - args += " " - args += "-m %s" % self._options.minDP - if self._options.maxDP : - args += " " - args += "-M %s" % self._options.maxDP - if self._options.bedFiles : - if self._options.bedFiles == "": - pass - else : - self._lBedFiles = self._options.bedFiles - cmd = "%s %s" %(prg, args) - - print cmd - - try: - tmp_err = tempfile.NamedTemporaryFile().name - tmp_stderr = open( tmp_err, 'wb' ) - proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stderr=tmp_stderr ) - returncode = proc.wait() - tmp_stderr.close() - # get stderr, allowing for case where it's very large - tmp_stderr = open( tmp_err, 'rb' ) - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() - if stderr: - raise Exception, stderr - except Exception, e: - self.stop_err( 'Error in VCFFiltering:\n' + str( e ) ) - - if True : - html = open(self._options.graphHTML, "w") - - os.mkdir(self._options.dirGraphs) - lGraphsFiles = glob.glob("VCFFiltering_graphs/*") - for file in lGraphsFiles : - baseName = os.path.basename(file) - shutil.move( file ,"%s/%s" %(self._options.dirGraphs, baseName)) - line = " \n" %(baseName) - html.write(line) - - -if __name__ == "__main__": - iWrapper = VCFFilteringWrapper() - iWrapper.setAttributesFromCmdLine() - iWrapper.run() diff -r a6b557df86db -r 3ca0f78f1102 VCFFiltering_wrapper.xml --- a/VCFFiltering_wrapper.xml Tue Dec 15 05:35:36 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,157 +0,0 @@ - - Filters SNP on a VCF depending on depth, allele number and allele frequency - - VCF_Gandalf_Tools - - - VCFFiltering.py --version - - - #if $DP_auto.is_DP_auto - VCFFiltering_wrapper.py -f $inputVCF -o $outputVCF -F $AF -N $AN - #else - VCFFiltering_wrapper.py -f $inputVCF -o $outputVCF -F $AF -N $AN -m $DP_auto.DPmin -M $DP_auto.DPmax - #end if - ## Bed files - #if $BedFile_List.is_BedFile - #for $bed in $BedFile_List.BedFiles - -b $bed.inputBed - #end for - #end if - --graphHTML $output_html --dirGraphs "$output_html.files_path" - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff -r a6b557df86db -r 3ca0f78f1102 VCFStorage_wrapper.py --- a/VCFStorage_wrapper.py Tue Dec 15 05:35:36 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,96 +0,0 @@ -#!/usr/bin/env python - - -import subprocess, tempfile, sys, os, glob, shutil, time, random -from optparse import OptionParser -from optparse import Option, OptionValueError - -class VCFStorageWrapper(object): - - def __init__(self): - self._options = None - - - def stop_err(self, msg ): - sys.stderr.write( "%s\n" % msg ) - sys.exit() - - - def setAttributesFromCmdLine(self): - description = "VCFStorage_wrapper" - description += "\nWrapper for VCFStorage\n VCFStorage " - description += "VCFStorage stores info from variant calling into a table. It will create a tabulate file with the different infos\n" - description += "example : VCFStorage -f fasta.fa -l genomelist.list -w workdir -o output.tab \n" - parser = OptionParser(description = description, version = "0.1") - parser.add_option("-f", "--fasta", dest = "fastaFile", action = "store", type = "string", help = "Input fasta file name [compulsory] [format: Fasta]", default = "") - parser.add_option("-l", "--genomeNameList", dest = "genomeNameList", action = "append", type = "string", help = "Input list of genome name ") - parser.add_option("-L", "--genomeFileList", dest = "genomeFileList", action = "append", type = "string", help = "Input list of genome VCF file ") - parser.add_option("-w", "--workDir", dest = "workDir", action = "store", type = "string", help = "name of the workingDirectory", default = "") - parser.add_option("-o", "--out", dest = "outFile", action = "store", type = "string", help = "Output file name [compulsory] [format: tab]", default = "") - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - - def _setAttributesFromOptions(self, options): - self._options = options - - def run(self): - self.createGenomeList() - cmd = self.createCmdLine() - self.launchCmdLine(cmd) - - def createGenomeList(self): - self.genomelistFile = "%s.genomeListFile" % self._options.outFile - lGenomeName = self._options.genomeNameList - lGenomeVCF = self._options.genomeFileList - output = open(self.genomelistFile, "w") - for i,genomeName in enumerate(lGenomeName) : - output.write("%s\t%s\n" % (lGenomeName[i],lGenomeVCF[i])) - output.close() - - def createCmdLine(self): - workdir = "VCFStorage_%s_%d" % (time.strftime("%d%H%M%S"), random.randint(0, 10000)) - prg = "VCFStorage.py" - args = "" - args += "-f %s" % self._options.fastaFile - args += " " - args += "-o %s" % self._options.outFile - args += " " - args += "-l %s" % self.genomelistFile - args += " " - args += "-w %s" % workdir - cmd = "%s %s" %(prg, args) - - print cmd - return cmd - - def launchCmdLine(self, cmd): - try: - tmp_err = tempfile.NamedTemporaryFile().name - tmp_stderr = open( tmp_err, 'wb' ) - proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stderr=tmp_stderr ) - returncode = proc.wait() - tmp_stderr.close() - # get stderr, allowing for case where it's very large - tmp_stderr = open( tmp_err, 'rb' ) - stderr = '' - buffsize = 1048576 - try: - while True: - stderr += tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() - if stderr: - raise Exception, stderr - except Exception, e: - os.remove(self.genomelistFile) - self.stop_err( 'Error in VCFStorage:\n' + str( e ) ) - os.remove(self.genomelistFile) - -if __name__ == "__main__": - iWrapper = VCFStorageWrapper() - iWrapper.setAttributesFromCmdLine() - iWrapper.run() diff -r a6b557df86db -r 3ca0f78f1102 VCFStorage_wrapper.xml --- a/VCFStorage_wrapper.xml Tue Dec 15 05:35:36 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,236 +0,0 @@ - - stores info from variant calling into a table. It will create a tabulate filed with SNP infos - - VCF_Gandalf_Tools - - - VCFStorage.py --version - - - VCFStorage_wrapper.py -f $inputFasta -o $outputVCFStorage - ## genome list - #for $VCF in $VCFFile - -l $VCF.strainName - -L $VCF.inputStrainVCF - #end for - - - - - - - - - - - - - - - - - - - - chr_17 - ccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaa - TACGCGCGCGCCTAACCCTACGACTTTAACCTACTCTAAACTCTCCTACTAGTACGTCTT - -VCF input file : :: - - ##fileformat=VCFv4.1 - ##fileDate=20140725 - ##source=freeBayes v0.9.13-2-ga830efd - ##reference=exmple.fsa - ##phasing=none - ##DetectedFormat=freebayes - ##FILTER= - ##FILTER= - ##FILTER= - ##FILTER= - ##FILTER= - #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT V1 - chr_17 17 . A G 529.213 G_AF;G_DP AB=0.583333;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=21;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=3.1137;EPPR=3.15506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=77.012;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=751;QR=535;RO=15;RPP=5.59539;RPPR=4.31318;RUN=1;SAF=11;SAP=3.1137;SAR=10;SRF=5;SRP=6.62942;SRR=10;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.58;G_DP=36;G_Base=G GT:DP:RO:QR:AO:QA:GL 0/1:36:15:535:21:751:-10,0,-10 - chr_17 37 . C G 1082.38 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=34;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=3.26577;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=48.0391;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1243;QR=0;RO=0;RPP=15.5282;RPPR=0;RUN=1;SAF=18;SAP=3.26577;SAR=16;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=34;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:34:0:0:34:1243:-10,-9.23017,0 - chr_17 40 . T T 825.518 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=29;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=6.67934;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.92992;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1082;QR=178;RO=5;RPP=9.07545;RPPR=13.8677;RUN=1;SAF=13;SAP=3.68421;SAR=16;SRF=5;SRP=13.8677;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.85;G_DP=34;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:34:5:178:29:1082:-10,0,-6.82575 - chr_17 60 . A . 699.741 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=22;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=17.2236;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=32.2544;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=823;QR=0;RO=0;RPP=9.32731;RPPR=0;RUN=1;SAF=12;SAP=3.40511;SAR=10;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=22;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:22:0:0:22:823:-10,-5.98732,0 - chr_17 73 . T . 846.299 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=27;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=16.6021;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=38.84;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1002;QR=0;RO=0;RPP=5.02092;RPPR=0;RUN=1;SAF=21;SAP=21.1059;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=27;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:27:0:0:27:1002:-10,-7.34226,0 - chr_17 81 . C T 764.464 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=25;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=13.5202;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=36.1324;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=902;QR=0;RO=0;RPP=3.79203;RPPR=0;RUN=1;SAF=19;SAP=17.6895;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=25;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:25:0:0:25:902:-10,-6.76842,0 - chr_17 105 . C T 1154 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=37;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.88603;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=52.0047;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1336;QR=0;RO=0;RPP=19.9713;RPPR=0;RUN=1;SAF=23;SAP=7.76406;SAR=14;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=37;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:37:0:0:37:1336:-10,-10,0 - chr_17 112 . G A 1276.25 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=40;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=10.8276;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=55.9501;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1471;QR=0;RO=0;RPP=10.8276;RPPR=0;RUN=1;SAF=26;SAP=10.8276;SAR=14;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=40;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:40:0:0:40:1471:-10,-10,0 - -expected result : :: - - CHROM POS reference V1 - chr_17 1 C U - chr_17 2 C U - chr_17 3 C U - chr_17 4 T U - chr_17 5 A U - chr_17 6 A U - chr_17 7 C U - chr_17 8 C U - chr_17 9 C U - chr_17 10 T U - chr_17 11 A U - chr_17 12 A U - chr_17 13 C U - chr_17 14 C U - chr_17 15 C U - chr_17 16 T U - chr_17 17 A F - chr_17 18 A U - chr_17 19 C U - chr_17 20 C U - chr_17 21 C U - chr_17 22 T U - chr_17 23 A U - chr_17 24 A U - chr_17 25 C U - chr_17 26 C U - chr_17 27 C U - chr_17 28 T U - chr_17 29 A U - chr_17 30 A U - chr_17 31 C U - chr_17 32 C U - chr_17 33 C U - chr_17 34 T U - chr_17 35 A U - chr_17 36 A U - chr_17 37 C G - chr_17 38 C U - chr_17 39 C U - chr_17 40 T F - chr_17 41 A U - chr_17 42 A U - chr_17 43 C U - chr_17 44 C U - chr_17 45 C U - chr_17 46 T U - chr_17 47 A U - chr_17 48 A U - chr_17 49 C U - chr_17 50 C U - chr_17 51 C U - chr_17 52 T U - chr_17 53 A U - chr_17 54 A U - chr_17 55 C U - chr_17 56 C U - chr_17 57 C U - chr_17 58 T U - chr_17 59 A U - chr_17 60 A R - chr_17 61 T U - chr_17 62 A U - chr_17 63 C U - chr_17 64 G U - chr_17 65 C U - chr_17 66 G U - chr_17 67 C U - chr_17 68 G U - chr_17 69 C U - chr_17 70 G U - chr_17 71 C U - chr_17 72 C U - chr_17 73 T R - chr_17 74 A U - chr_17 75 A U - chr_17 76 C U - chr_17 77 C U - chr_17 78 C U - chr_17 79 T U - chr_17 80 A U - chr_17 81 C T - chr_17 82 G U - chr_17 83 A U - chr_17 84 C U - chr_17 85 T U - chr_17 86 T U - chr_17 87 T U - chr_17 88 A U - chr_17 89 A U - chr_17 90 C U - chr_17 91 C U - chr_17 92 T U - chr_17 93 A U - chr_17 94 C U - chr_17 95 T U - chr_17 96 C U - chr_17 97 T U - chr_17 98 A U - chr_17 99 A U - chr_17 100 A U - chr_17 101 C U - chr_17 102 T U - chr_17 103 C U - chr_17 104 T U - chr_17 105 C F - chr_17 106 C U - chr_17 107 T U - chr_17 108 A U - chr_17 109 C U - chr_17 110 T U - chr_17 111 A U - chr_17 112 G F - chr_17 113 T U - chr_17 114 A U - chr_17 115 C U - chr_17 116 G U - chr_17 117 T U - chr_17 118 C U - chr_17 119 T U - chr_17 120 T U - ------ - -**reference :** - -]]> - - diff -r a6b557df86db -r 3ca0f78f1102 repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Tue Dec 15 05:38:37 2015 -0500 @@ -0,0 +1,10 @@ + + + + + + + + + + diff -r a6b557df86db -r 3ca0f78f1102 test-data/Expchr17.tab --- a/test-data/Expchr17.tab Tue Dec 15 05:35:36 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,121 +0,0 @@ -CHROM POS reference V1 -chr_17 1 C U -chr_17 2 C U -chr_17 3 C U -chr_17 4 T U -chr_17 5 A U -chr_17 6 A U -chr_17 7 C U -chr_17 8 C U -chr_17 9 C U -chr_17 10 T U -chr_17 11 A U -chr_17 12 A U -chr_17 13 C U -chr_17 14 C U -chr_17 15 C U -chr_17 16 T U -chr_17 17 A F -chr_17 18 A U -chr_17 19 C U -chr_17 20 C U -chr_17 21 C U -chr_17 22 T U -chr_17 23 A U -chr_17 24 A U -chr_17 25 C U -chr_17 26 C U -chr_17 27 C U -chr_17 28 T U -chr_17 29 A U -chr_17 30 A U -chr_17 31 C U -chr_17 32 C U -chr_17 33 C U -chr_17 34 T U -chr_17 35 A U -chr_17 36 A U -chr_17 37 C G -chr_17 38 C U -chr_17 39 C U -chr_17 40 T F -chr_17 41 A U -chr_17 42 A U -chr_17 43 C U -chr_17 44 C U -chr_17 45 C U -chr_17 46 T U -chr_17 47 A U -chr_17 48 A U -chr_17 49 C U -chr_17 50 C U -chr_17 51 C U -chr_17 52 T U -chr_17 53 A U -chr_17 54 A U -chr_17 55 C U -chr_17 56 C U -chr_17 57 C U -chr_17 58 T U -chr_17 59 A U -chr_17 60 A R -chr_17 61 T U -chr_17 62 A U -chr_17 63 C U -chr_17 64 G U -chr_17 65 C U -chr_17 66 G U -chr_17 67 C U -chr_17 68 G U -chr_17 69 C U -chr_17 70 G U -chr_17 71 C U -chr_17 72 C U -chr_17 73 T R -chr_17 74 A U -chr_17 75 A U -chr_17 76 C U -chr_17 77 C U -chr_17 78 C U -chr_17 79 T U -chr_17 80 A U -chr_17 81 C T -chr_17 82 G U -chr_17 83 A U -chr_17 84 C U -chr_17 85 T U -chr_17 86 T U -chr_17 87 T U -chr_17 88 A U -chr_17 89 A U -chr_17 90 C U -chr_17 91 C U -chr_17 92 T U -chr_17 93 A U -chr_17 94 C U -chr_17 95 T U -chr_17 96 C U -chr_17 97 T U -chr_17 98 A U -chr_17 99 A U -chr_17 100 A U -chr_17 101 C U -chr_17 102 T U -chr_17 103 C U -chr_17 104 T U -chr_17 105 C F -chr_17 106 C U -chr_17 107 T U -chr_17 108 A U -chr_17 109 C U -chr_17 110 T U -chr_17 111 A U -chr_17 112 G F -chr_17 113 T U -chr_17 114 A U -chr_17 115 C U -chr_17 116 G U -chr_17 117 T U -chr_17 118 C U -chr_17 119 T U -chr_17 120 T U diff -r a6b557df86db -r 3ca0f78f1102 test-data/VCFCarto_input.tab --- a/test-data/VCFCarto_input.tab Tue Dec 15 05:35:36 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,76 +0,0 @@ -CHROM POS reference REF1 G01 REF2 G02 G03 G04 G05 G06 G07 G08 G09 G10 G11 G12 -Chr1 1 A R R R R U R R R R R R R R R -Chr1 2 T R R R R R U R R R R R R R R -Chr1 3 G R R R R R R R R R R R R R R -Chr1 4 G R R R R R R R R R R R R F R -Chr1 5 G R R R R R R U F R R R R R R -Chr1 6 C R R R R R R R R R R R R R U -Chr1 7 A G C C C F C C C C C G C G G -Chr1 8 G R R R R R R R R R R R R R R -Chr1 9 C R T T R T T T U R T R T T T -Chr1 10 T R R R R R R R R R R R R R U -Chr1 11 T R R R R R R R R R R R F R R -Chr1 12 A R R R R U R R R R F R R R R -Chr1 13 A R R G G R F R F G R G R R F -Chr1 14 A R R R R R R R R F R R R R R -Chr1 15 G R R R U R F R R R R R R U U -Chr1 16 G A R R A R R U F R R A A R A -Chr1 17 A R G G R U R R G G R G U R G -Chr1 18 C R R R R R U R R R R R R R R -Chr1 19 G C U R C R C U R R C C C R C -Chr1 20 G A U R A R A U R R A A A R A -Chr1 21 G T U R T R T U R R T T T R T -Chr1 22 A T U R T R T U R R T T T R T -Chr1 23 C T T R T R R R T R U T R T T -Chr1 24 T R R R R R U R R R R R R R F -Chr1 25 G R F R R R R R U R F R R R R -Chr1 26 T R R C C C C C R R C R C R U -Chr1 27 C R R G G G G R G R G R G R R -Chr1 28 C G T T T G G T T F T G T T G -Chr1 29 G T R R R R T R T R T T R T R -Chr1 30 T R R R R R R R R R R R R R R -Chr1 31 A R R R R F R R R R F R R R R -Chr1 32 A G G R G G G R R G G G G G R -Chr1 33 G R R R R R R R R R R R R R R -Chr1 34 C R R R R R R R R R R R R R R -Chr1 35 C R R R R R F R R R R R R R U -Chr2 1 T R R R F R R R R R R R R R R -Chr2 2 A C R R C C U R R R R C C C U -Chr2 3 C R R R R R R U R R R R R R R -Chr2 4 C R R R R R R R U R R R R F R -Chr2 5 T R R R R R R R R R R R R R R -Chr2 6 C R R R R R R R R R R R R R R -Chr2 7 A T F R U R T T T R T T F T T -Chr2 8 T R R R R R R R R R R R R R R -Chr2 9 C R R R R R R R R R R R R R R -Chr2 10 G R T T T T R T R R R R R U R -Chr2 11 C R A A A A R A R R R R R U R -Chr2 12 A R T T T T R T R R R R R U R -Chr2 13 T R C C C C R C R R R R R U R -Chr2 14 C T A A T A T A T A T T A A A -Chr2 15 T R R R F R R R R R R R R R R -Chr2 16 A R R R R R R R U R R R R R R -Chr2 17 A R U R R R R R R R R R R R F -Chr2 18 G R R R R R R R R R R R R R R -Chr2 19 A R R R R R R F R R R R R R R -Chr2 20 C R R R R R R R F R R R R R R -Chr2 21 G A R R A A A R R R A A R R R -Chr2 22 A R R R R R R F R R R R R R R -Chr2 23 A R R T T R R T T T T T R R R -Chr2 24 T R R R R R R U R R R R R R F -Chr2 25 T R A A R R A R A R R A R R A -Chr2 26 G R R R R R R R R R R R R R R -Chr2 27 A R R R R R R R R R R R R U R -Chr2 28 C R U R R F F R R F R F U R R -Chr2 29 G R R R R R R F R R R R R R R -Chr2 30 T A A G A G G A A G F G G G U -Chr2 31 A R R R R R R R R U U R R R R -Chr2 32 G R R R R R R U U R R R R R R -Chr2 33 G R U R R R R U R R R R R R R -Chr2 34 A R R R U R R R R R R R R R R -Chr2 35 G R R R R R R R R R R R R R R -Chr2 36 T R R R R R R U R R R R R R R -Chr3 1 T U R R R R R U R R R R R R R -Chr3 2 T R R U R R R U R R R R R R R -Chr3 3 T F R R R R R U R R R R R R R -Chr3 4 T R R F R R R U R R R R R R R diff -r a6b557df86db -r 3ca0f78f1102 test-data/VCFCarto_output.tab --- a/test-data/VCFCarto_output.tab Tue Dec 15 05:35:36 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,27 +0,0 @@ -CHROM POS reference REF1 G01 REF2 G02 G03 G04 G05 G06 G07 G08 G09 G10 G11 G12 -Chr1 7 A G C C C F C C C C C G C G G -Chr1 9 C R T T R T T T U R T R T T T -Chr1 13 A R R G G R F R F G R G R R F -Chr1 16 G A R R A R R U F R R A A R A -Chr1 17 A R G G R U R R G G R G U R G -Chr1 19 G C U R C R C U R R C C C R C -Chr1 20 G A U R A R A U R R A A A R A -Chr1 21 G T U R T R T U R R T T T R T -Chr1 22 A T U R T R T U R R T T T R T -Chr1 23 C T T R T R R R T R U T R T T -Chr1 26 T R R C C C C C R R C R C R U -Chr1 27 C R R G G G G R G R G R G R R -Chr1 28 C G T T T G G T T F T G T T G -Chr1 29 G T R R R R T R T R T T R T R -Chr1 32 A G G R G G G R R G G G G G R -Chr2 2 A C R R C C U R R R R C C C U -Chr2 7 A T F R U R T T T R T T F T T -Chr2 10 G R T T T T R T R R R R R U R -Chr2 11 C R A A A A R A R R R R R U R -Chr2 12 A R T T T T R T R R R R R U R -Chr2 13 T R C C C C R C R R R R R U R -Chr2 14 C T A A T A T A T A T T A A A -Chr2 21 G A R R A A A R R R A A R R R -Chr2 23 A R R T T R R T T T T T R R R -Chr2 25 T R A A R R A R A R R A R R A -Chr2 30 T A A G A G G A A G F G G G U diff -r a6b557df86db -r 3ca0f78f1102 test-data/VCFCarto_output_merged.bed --- a/test-data/VCFCarto_output_merged.bed Tue Dec 15 05:35:36 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,20 +0,0 @@ -Chr1 7 7 *M_00001 -Chr1 9 9 *M_00002 -Chr1 13 13 *M_00003 -Chr1 16 16 *M_00004 -Chr1 17 17 *M_00005 -Chr1 19 22 *M_00006 -Chr1 23 23 *M_00007 -Chr1 26 26 *M_00008 -Chr1 27 27 *M_00009 -Chr1 28 28 *M_00010 -Chr1 29 29 *M_00011 -Chr1 32 32 *M_00012 -Chr2 2 2 *M_00013 -Chr2 7 7 *M_00014 -Chr2 10 13 *M_00015 -Chr2 14 14 *M_00016 -Chr2 21 21 *M_00017 -Chr2 23 23 *M_00018 -Chr2 25 25 *M_00019 -Chr2 30 30 *M_00020 diff -r a6b557df86db -r 3ca0f78f1102 test-data/VCFCarto_output_merged.tab --- a/test-data/VCFCarto_output_merged.tab Tue Dec 15 05:35:36 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -CHROM POS reference REF1 G01 REF2 G02 G03 G04 G05 G06 G07 G08 G09 G10 G11 G12 -Chr1 *M_00001 - A H H H - H H H H H A H A A -Chr1 *M_00002 - A H H A H H H - A H A H H H -Chr1 *M_00003 - A A H H A - A - H A H A A - -Chr1 *M_00004 - A H H A H H - - H H A A H A -Chr1 *M_00005 - A H H A - A A H H A H - A H -Chr1 *M_00006 - A - H A H A - H H A A A H A -Chr1 *M_00007 - A A H A H H H A H - A H A A -Chr1 *M_00008 - A A H H H H H A A H A H A - -Chr1 *M_00009 - A A H H H H A H A H A H A A -Chr1 *M_00010 - A H H H A A H H - H A H H A -Chr1 *M_00011 - A H H H H A H A H A A H A H -Chr1 *M_00012 - A A H A A A H H A A A A A H -Chr2 *M_00013 - A H H A A - H H H H A A A - -Chr2 *M_00014 - A - H - H A A A H A A - A A -Chr2 *M_00015 - A H H H H A H A A A A A - A -Chr2 *M_00016 - A H H A H A H A H A A H H H -Chr2 *M_00017 - A H H A A A H H H A A H H H -Chr2 *M_00018 - A A H H A A H H H H H A A A -Chr2 *M_00019 - A H H A A H A H A A H A A H -Chr2 *M_00020 - A A H A H H A A H - H H H - diff -r a6b557df86db -r 3ca0f78f1102 test-data/VCFFiltering_DP_4_200_output.vcf --- a/test-data/VCFFiltering_DP_4_200_output.vcf Tue Dec 15 05:35:36 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,110 +0,0 @@ -##fileformat=VCFv4.1 -##fileDate=20140725 -##source=freeBayes v0.9.13-2-ga830efd -##phasing=none -##DetectedFormat=freebayes -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G15_myco -chr_1 235 . C T 21.392 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=0.865778;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=35;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:77:-4.63556,0,-2.351 -chr_1 244 . C T 21.1881 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=0.865718;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=35;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:76:-4.61503,0,-2.35102 -chr_1 253 . T C 73.475 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=34;MQMR=0;NS=1;NUMALT=1;ODDS=7.23646;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-8.62509,-0.841726,0 -chr_1 333 . G A 24.2337 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=3.07477;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=82;QR=24;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:1:24:2:82:-4.69685,0,-1.39164 -chr_1 354 . G A 20.5104 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=2.23682;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=28;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:1:28:2:78:-4.66174,0,-1.75556 -chr_1 363 . G A 40.3032 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36;MQMR=0;NS=1;NUMALT=1;ODDS=5.91856;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:63:-5.23324,-0.570398,0 -chr_1 1531 . G A 73.2764 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=0;NS=1;NUMALT=1;ODDS=7.23732;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=115;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:115:-9.08235,-0.842098,0 -chr_1 1565 . A G 14.5726 G_AF AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=38;MQMR=35;NS=1;NUMALT=1;ODDS=3.30493;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=71;RO=2;RPP=7.35324;RPPR=3.0103;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.50;G_DP=4;G_Base=G GT:DP:RO:QR:AO:QA:GL 0/1:4:2:71:2:71:-5.0654,0,-4.84835 -chr_1 1589 . A G 102.964 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36.5;MQMR=0;NS=1;NUMALT=1;ODDS=8.55461;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=155;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:155:-10,-1.11316,0 -chr_1 1635 . G A 95.7333 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=38.5;MQMR=0;NS=1;NUMALT=1;ODDS=8.55365;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=141;QR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:141:-10,-1.11274,0 -chr_1 2624 . C T 122.967 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=44.75;MQMR=0;NS=1;NUMALT=1;ODDS=8.5553;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=156;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:156:-10,-1.11346,0 -chr_1 2670 . C T 30.7231 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.739044;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:41:2:71:-5.60946,0,-2.40604 -chr_1 2671 . G A 30.0349 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.738983;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:1:41:2:70:-5.5406,0,-2.40606 -chr_1 2686 . A G 28.1218 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.861385;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=39;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:3:1:39:2:67:-5.31237,0,-2.3529 -chr_1 2697 . G A 66.8365 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23789;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=104;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:104:-9.39261,-0.842345,0 -chr_1 2699 . G A 75.6507 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23781;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=103;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:103:-9.31979,-0.842311,0 -chr_1 2747 . C T 52.6764 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=5.92179;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=81;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:81:-7.07265,-0.5718,0 -chr_1 3616 . C T 96.527 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=11.6962;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=8.55506;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=153;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:153:-10,-1.11336,0 -chr_1 3624 . A G 99.7577 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=11.6962;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=8.55532;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=158;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:158:-10,-1.11347,0 -chr_1 3630 . G A 119.888 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=13.8677;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=9.87182;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=191;QR=0;RO=0;RPP=13.8677;RPPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:191:-10,-1.38419,0 -chr_1 3657 . T C 146.729 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=9.87224;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=204;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:204:-10,-1.38437,0 -chr_1 3681 . C T 141.607 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=8.80089;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.5;MQMR=0;NS=1;NUMALT=1;ODDS=11.1867;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=201;QR=0;RO=0;RPP=8.80089;RPPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=6;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:201:-10,-1.65422,0 -chr_1 3746 . G A 143.027 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=42.8;MQMR=0;NS=1;NUMALT=1;ODDS=9.87133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=177;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=2;SAP=3.44459;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:177:-10,-1.38398,0 -chr_1 3766 . TGG TG 207.378 InDel AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1M1D1M;DP=7;DPB=4.66667;DPRA=0;EPP=3.32051;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.8571;MQMR=0;NS=1;NUMALT=1;ODDS=12.5052;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=267;QR=0;RO=0;RPP=3.32051;RPPR=0;RUN=1;SAF=1;SAP=10.7656;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=del;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=7;G_Base=TG GT:DP:RO:QR:AO:QA:GL 1/1:7:0:0:7:267:-10,-1.9258,0 -chr_1 3804 . C T 168.638 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=4.45795;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=42.1667;MQMR=0;NS=1;NUMALT=1;ODDS=11.188;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=213;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=1;SAP=8.80089;SAR=5;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=6;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:213:-10,-1.65476,0 -chr_1 3845 . G A 130.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=6.91895;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.8;MQMR=0;NS=1;NUMALT=1;ODDS=9.87163;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=184;QR=0;RO=0;RPP=13.8677;RPPR=0;RUN=1;SAF=1;SAP=6.91895;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:184:-10,-1.38411,0 -chr_1 3857 . G A 72.7109 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23836;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=113;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:113:-9.98004,-0.84255,0 -chr_1 4299 . C T 48.7928 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.73412;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=48;NS=1;NUMALT=1;ODDS=2.04069;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=100;QR=34;RO=1;RPP=9.52472;RPPR=5.18177;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.75;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:1:34:3:100:-7.69498,0,-2.01683 -chr_1 4311 . A G 138.174 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=6.91895;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40.2;MQMR=0;NS=1;NUMALT=1;ODDS=9.8711;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=179;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=3;SAP=3.44459;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:179:-10,-1.38387,0 -chr_1 4357 . C T 141.385 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40.2;MQMR=0;NS=1;NUMALT=1;ODDS=9.87061;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=181;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=2;SAP=3.44459;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:181:-10,-1.38366,0 -chr_1 4372 . C T 57.8383 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.73412;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=48;NS=1;NUMALT=1;ODDS=0.86483;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=40;RO=1;RPP=3.73412;RPPR=5.18177;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.75;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:1:40:3:110:-8.53351,0,-2.5275 -chr_1 4389 . C T 176.339 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.80219;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=45.4286;MQMR=48;NS=1;NUMALT=1;ODDS=6.11702;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=247;QR=37;RO=1;RPP=3.32051;RPPR=5.18177;RUN=1;SAF=3;SAP=3.32051;SAR=4;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.88;G_DP=8;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:8:1:37:7:247:-10,0,-1.14959 -chr_1 4398 . T C 197.868 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=5.80219;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=45.4286;MQMR=0;NS=1;NUMALT=1;ODDS=12.5039;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=243;QR=0;RO=0;RPP=3.32051;RPPR=0;RUN=1;SAF=3;SAP=3.32051;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=7;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:7:0:0:7:243:-10,-1.92523,0 -chr_1 4404 . T C 168.543 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=4.45795;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=46.3333;MQMR=0;NS=1;NUMALT=1;ODDS=11.1873;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=209;QR=0;RO=0;RPP=4.45795;RPPR=0;RUN=1;SAF=2;SAP=4.45795;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=6;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:209:-10,-1.65448,0 -chr_1 4475 . C T 81.0612 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=47;MQMR=0;NS=1;NUMALT=1;ODDS=7.2379;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-9.86084,-0.842352,0 -chr_1 4540 . C T 72.5101 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23698;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=101;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:101:-9.00573,-0.841952,0 -chr_1 4580 . C T 81.3345 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23817;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=119;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:119:-9.88816,-0.842465,0 -chr_1 4611 . C G 51.9857 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.5;MQMR=0;NS=1;NUMALT=1;ODDS=5.92133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=69;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:69:-6.40152,-0.5716,0 -chr_1 4661 . A G 19.7502 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=43;NS=1;NUMALT=1;ODDS=0.834078;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=35;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:76:-5.08162,0,-2.36476 -chr_1 4678 . G A 21.951 G_AF;G_DP AB=0.666667;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=43;NS=1;NUMALT=1;ODDS=0.136458;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 0/1:3:1:41:2:68:-4.94794,0,-2.78626 -chr_1 4686 . C T 81.6957 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23731;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-9.44717,-0.842096,0 -chr_1 4699 . G A 103.379 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36.75;MQMR=0;NS=1;NUMALT=1;ODDS=8.55324;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=140;QR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:140:-10,-1.11256,0 -chr_1 4717 . C T 18.6085 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=34;NS=1;NUMALT=1;ODDS=1.12012;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=40;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:40:2:66:-4.87583,0,-2.24054 -chr_1 4727 . G A 43.4619 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=32;MQMR=0;NS=1;NUMALT=1;ODDS=5.91984;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:66:-5.54913,-0.570955,0 -chr_1 4747 . C T 40.3421 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=34;MQMR=0;NS=1;NUMALT=1;ODDS=5.92045;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:68:-5.83919,-0.571218,0 -chr_1 3305168 . T A,G 280.615 G_AF AB=0.75,0.25;ABP=9.52472,9.52472;AC=1,1;AF=0.5,0.5;AN=2;AO=9,3;CIGAR=1X,1X;DP=12;DPB=12;DPRA=0,0;EPP=9.04217,3.73412;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=4.632;PAIRED=1,1;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=319,107;QR=0;RO=0;RPP=9.04217,9.52472;RPPR=0;RUN=1,1;SAF=4,2;SAP=3.25157,3.73412;SAR=5,1;SRF=0;SRP=0;SRR=0;TYPE=snp,snp;technology.illumina=1,1;G_AN=2;G_AF=0.75;G_DP=12;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/2:12:0:0:9,3:319,107:-10,-8.89435,-6.43456,-10,0,-10 -chr_1 3305169 . T A,G 280.615 G_AF AB=0.25,0.75;ABP=9.52472,9.52472;AC=1,1;AF=0.5,0.5;AN=2;AO=9,3;CIGAR=1X,1X;DP=12;DPB=12;DPRA=0,0;EPP=9.04217,3.73412;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=4.632;PAIRED=1,1;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=319,107;QR=0;RO=0;RPP=9.04217,9.52472;RPPR=0;RUN=1,1;SAF=4,2;SAP=3.25157,3.73412;SAR=5,1;SRF=0;SRP=0;SRR=0;TYPE=snp,snp;technology.illumina=1,1;G_AN=2;G_AF=0.75;G_DP=12;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/2:12:0:0:9,3:319,107:-10,-8.89435,-6.43456,-10,0,-10 diff -r a6b557df86db -r 3ca0f78f1102 test-data/VCFFiltering_DPauto_output.vcf --- a/test-data/VCFFiltering_DPauto_output.vcf Tue Dec 15 05:35:36 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,110 +0,0 @@ -##fileformat=VCFv4.1 -##fileDate=20140725 -##source=freeBayes v0.9.13-2-ga830efd -##phasing=none -##DetectedFormat=freebayes -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G15_myco -chr_1 235 . C T 21.392 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=0.865778;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=35;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:77:-4.63556,0,-2.351 -chr_1 244 . C T 21.1881 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=0.865718;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=35;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:76:-4.61503,0,-2.35102 -chr_1 253 . T C 73.475 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=34;MQMR=0;NS=1;NUMALT=1;ODDS=7.23646;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-8.62509,-0.841726,0 -chr_1 333 . G A 24.2337 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=3.07477;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=82;QR=24;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:1:24:2:82:-4.69685,0,-1.39164 -chr_1 354 . G A 20.5104 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=2.23682;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=28;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:1:28:2:78:-4.66174,0,-1.75556 -chr_1 363 . G A 40.3032 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36;MQMR=0;NS=1;NUMALT=1;ODDS=5.91856;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:63:-5.23324,-0.570398,0 -chr_1 1531 . G A 73.2764 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=0;NS=1;NUMALT=1;ODDS=7.23732;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=115;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:115:-9.08235,-0.842098,0 -chr_1 1565 . A G 14.5726 G_AF AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=38;MQMR=35;NS=1;NUMALT=1;ODDS=3.30493;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=71;RO=2;RPP=7.35324;RPPR=3.0103;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.50;G_DP=4;G_Base=G GT:DP:RO:QR:AO:QA:GL 0/1:4:2:71:2:71:-5.0654,0,-4.84835 -chr_1 1589 . A G 102.964 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36.5;MQMR=0;NS=1;NUMALT=1;ODDS=8.55461;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=155;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:155:-10,-1.11316,0 -chr_1 1635 . G A 95.7333 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=38.5;MQMR=0;NS=1;NUMALT=1;ODDS=8.55365;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=141;QR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:141:-10,-1.11274,0 -chr_1 2624 . C T 122.967 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=44.75;MQMR=0;NS=1;NUMALT=1;ODDS=8.5553;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=156;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:156:-10,-1.11346,0 -chr_1 2670 . C T 30.7231 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.739044;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:41:2:71:-5.60946,0,-2.40604 -chr_1 2671 . G A 30.0349 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.738983;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:1:41:2:70:-5.5406,0,-2.40606 -chr_1 2686 . A G 28.1218 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.861385;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=39;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:3:1:39:2:67:-5.31237,0,-2.3529 -chr_1 2697 . G A 66.8365 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23789;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=104;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:104:-9.39261,-0.842345,0 -chr_1 2699 . G A 75.6507 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23781;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=103;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:103:-9.31979,-0.842311,0 -chr_1 2747 . C T 52.6764 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=5.92179;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=81;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:81:-7.07265,-0.5718,0 -chr_1 3616 . C T 96.527 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=11.6962;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=8.55506;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=153;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:153:-10,-1.11336,0 -chr_1 3624 . A G 99.7577 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=11.6962;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=8.55532;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=158;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:158:-10,-1.11347,0 -chr_1 3630 . G A 119.888 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=13.8677;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=9.87182;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=191;QR=0;RO=0;RPP=13.8677;RPPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:191:-10,-1.38419,0 -chr_1 3657 . T C 146.729 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=9.87224;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=204;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:204:-10,-1.38437,0 -chr_1 3681 . C T 141.607 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=8.80089;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.5;MQMR=0;NS=1;NUMALT=1;ODDS=11.1867;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=201;QR=0;RO=0;RPP=8.80089;RPPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=6;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:201:-10,-1.65422,0 -chr_1 3746 . G A 143.027 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=42.8;MQMR=0;NS=1;NUMALT=1;ODDS=9.87133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=177;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=2;SAP=3.44459;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:177:-10,-1.38398,0 -chr_1 3766 . TGG TG 207.378 InDel;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1M1D1M;DP=7;DPB=4.66667;DPRA=0;EPP=3.32051;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.8571;MQMR=0;NS=1;NUMALT=1;ODDS=12.5052;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=267;QR=0;RO=0;RPP=3.32051;RPPR=0;RUN=1;SAF=1;SAP=10.7656;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=del;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=7;G_Base=TG GT:DP:RO:QR:AO:QA:GL 1/1:7:0:0:7:267:-10,-1.9258,0 -chr_1 3804 . C T 168.638 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=4.45795;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=42.1667;MQMR=0;NS=1;NUMALT=1;ODDS=11.188;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=213;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=1;SAP=8.80089;SAR=5;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=6;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:213:-10,-1.65476,0 -chr_1 3845 . G A 130.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=6.91895;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.8;MQMR=0;NS=1;NUMALT=1;ODDS=9.87163;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=184;QR=0;RO=0;RPP=13.8677;RPPR=0;RUN=1;SAF=1;SAP=6.91895;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:184:-10,-1.38411,0 -chr_1 3857 . G A 72.7109 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23836;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=113;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:113:-9.98004,-0.84255,0 -chr_1 4299 . C T 48.7928 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.73412;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=48;NS=1;NUMALT=1;ODDS=2.04069;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=100;QR=34;RO=1;RPP=9.52472;RPPR=5.18177;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.75;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:1:34:3:100:-7.69498,0,-2.01683 -chr_1 4311 . A G 138.174 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=6.91895;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40.2;MQMR=0;NS=1;NUMALT=1;ODDS=9.8711;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=179;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=3;SAP=3.44459;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:179:-10,-1.38387,0 -chr_1 4357 . C T 141.385 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40.2;MQMR=0;NS=1;NUMALT=1;ODDS=9.87061;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=181;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=2;SAP=3.44459;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=5;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:181:-10,-1.38366,0 -chr_1 4372 . C T 57.8383 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.73412;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=48;NS=1;NUMALT=1;ODDS=0.86483;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=40;RO=1;RPP=3.73412;RPPR=5.18177;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.75;G_DP=4;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:4:1:40:3:110:-8.53351,0,-2.5275 -chr_1 4389 . C T 176.339 G_AF;G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.80219;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=45.4286;MQMR=48;NS=1;NUMALT=1;ODDS=6.11702;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=247;QR=37;RO=1;RPP=3.32051;RPPR=5.18177;RUN=1;SAF=3;SAP=3.32051;SAR=4;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.88;G_DP=8;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:8:1:37:7:247:-10,0,-1.14959 -chr_1 4398 . T C 197.868 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=5.80219;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=45.4286;MQMR=0;NS=1;NUMALT=1;ODDS=12.5039;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=243;QR=0;RO=0;RPP=3.32051;RPPR=0;RUN=1;SAF=3;SAP=3.32051;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=7;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:7:0:0:7:243:-10,-1.92523,0 -chr_1 4404 . T C 168.543 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=4.45795;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=46.3333;MQMR=0;NS=1;NUMALT=1;ODDS=11.1873;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=209;QR=0;RO=0;RPP=4.45795;RPPR=0;RUN=1;SAF=2;SAP=4.45795;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=6;G_Base=C GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:209:-10,-1.65448,0 -chr_1 4475 . C T 81.0612 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=47;MQMR=0;NS=1;NUMALT=1;ODDS=7.2379;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-9.86084,-0.842352,0 -chr_1 4540 . C T 72.5101 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23698;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=101;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:101:-9.00573,-0.841952,0 -chr_1 4580 . C T 81.3345 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23817;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=119;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:119:-9.88816,-0.842465,0 -chr_1 4611 . C G 51.9857 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.5;MQMR=0;NS=1;NUMALT=1;ODDS=5.92133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=69;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:69:-6.40152,-0.5716,0 -chr_1 4661 . A G 19.7502 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=43;NS=1;NUMALT=1;ODDS=0.834078;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=35;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:76:-5.08162,0,-2.36476 -chr_1 4678 . G A 21.951 G_AF AB=0.666667;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=43;NS=1;NUMALT=1;ODDS=0.136458;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=A GT:DP:RO:QR:AO:QA:GL 0/1:3:1:41:2:68:-4.94794,0,-2.78626 -chr_1 4686 . C T 81.6957 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23731;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-9.44717,-0.842096,0 -chr_1 4699 . G A 103.379 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36.75;MQMR=0;NS=1;NUMALT=1;ODDS=8.55324;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=140;QR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=4;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:140:-10,-1.11256,0 -chr_1 4717 . C T 18.6085 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=34;NS=1;NUMALT=1;ODDS=1.12012;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=40;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.67;G_DP=3;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:3:1:40:2:66:-4.87583,0,-2.24054 -chr_1 4727 . G A 43.4619 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=32;MQMR=0;NS=1;NUMALT=1;ODDS=5.91984;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:66:-5.54913,-0.570955,0 -chr_1 4747 . C T 40.3421 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=34;MQMR=0;NS=1;NUMALT=1;ODDS=5.92045;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=2;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:68:-5.83919,-0.571218,0 -chr_1 3305168 . T A,G 280.615 G_AF;G_DP AB=0.75,0.25;ABP=9.52472,9.52472;AC=1,1;AF=0.5,0.5;AN=2;AO=9,3;CIGAR=1X,1X;DP=12;DPB=12;DPRA=0,0;EPP=9.04217,3.73412;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=4.632;PAIRED=1,1;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=319,107;QR=0;RO=0;RPP=9.04217,9.52472;RPPR=0;RUN=1,1;SAF=4,2;SAP=3.25157,3.73412;SAR=5,1;SRF=0;SRP=0;SRR=0;TYPE=snp,snp;technology.illumina=1,1;G_AN=2;G_AF=0.75;G_DP=12;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/2:12:0:0:9,3:319,107:-10,-8.89435,-6.43456,-10,0,-10 -chr_1 3305169 . T A,G 280.615 G_AF;G_DP AB=0.25,0.75;ABP=9.52472,9.52472;AC=1,1;AF=0.5,0.5;AN=2;AO=9,3;CIGAR=1X,1X;DP=12;DPB=12;DPRA=0,0;EPP=9.04217,3.73412;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=4.632;PAIRED=1,1;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=319,107;QR=0;RO=0;RPP=9.04217,9.52472;RPPR=0;RUN=1,1;SAF=4,2;SAP=3.25157,3.73412;SAR=5,1;SRF=0;SRP=0;SRR=0;TYPE=snp,snp;technology.illumina=1,1;G_AN=2;G_AF=0.75;G_DP=12;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/2:12:0:0:9,3:319,107:-10,-8.89435,-6.43456,-10,0,-10 diff -r a6b557df86db -r 3ca0f78f1102 test-data/VCFFiltering_input.vcf --- a/test-data/VCFFiltering_input.vcf Tue Dec 15 05:35:36 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,100 +0,0 @@ -##fileformat=VCFv4.1 -##fileDate=20140725 -##source=freeBayes v0.9.13-2-ga830efd -##phasing=none -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##INFO= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -##FORMAT= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT G15_myco -chr_1 235 . C T 21.392 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=0.865778;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=77;QR=35;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:77:-4.63556,0,-2.351 -chr_1 244 . C T 21.1881 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=0.865718;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=35;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:76:-4.61503,0,-2.35102 -chr_1 253 . T C 73.475 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=34;MQMR=0;NS=1;NUMALT=1;ODDS=7.23646;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-8.62509,-0.841726,0 -chr_1 333 . G A 24.2337 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=3.07477;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=82;QR=24;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:24:2:82:-4.69685,0,-1.39164 -chr_1 354 . G A 20.5104 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=30;MQMR=42;NS=1;NUMALT=1;ODDS=2.23682;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=78;QR=28;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:28:2:78:-4.66174,0,-1.75556 -chr_1 363 . G A 40.3032 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36;MQMR=0;NS=1;NUMALT=1;ODDS=5.91856;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=63;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:63:-5.23324,-0.570398,0 -chr_1 1531 . G A 73.2764 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=0;NS=1;NUMALT=1;ODDS=7.23732;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=115;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=3;SAP=9.52472;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:115:-9.08235,-0.842098,0 -chr_1 1565 . A G 14.5726 . AB=0.5;ABP=3.0103;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=7.35324;EPPR=7.35324;GTI=0;LEN=1;MEANALT=1;MQM=38;MQMR=35;NS=1;NUMALT=1;ODDS=3.30493;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=71;RO=2;RPP=7.35324;RPPR=3.0103;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=1;SRP=3.0103;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 0/1:4:2:71:2:71:-5.0654,0,-4.84835 -chr_1 1589 . A G 102.964 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36.5;MQMR=0;NS=1;NUMALT=1;ODDS=8.55461;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=155;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=1;SAP=5.18177;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:155:-10,-1.11316,0 -chr_1 1635 . G A 95.7333 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=38.5;MQMR=0;NS=1;NUMALT=1;ODDS=8.55365;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=141;QR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAF=0;SAP=11.6962;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:141:-10,-1.11274,0 -chr_1 2624 . C T 122.967 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=5.18177;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=44.75;MQMR=0;NS=1;NUMALT=1;ODDS=8.5553;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=156;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:156:-10,-1.11346,0 -chr_1 2670 . C T 30.7231 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.739044;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=71;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:41:2:71:-5.60946,0,-2.40604 -chr_1 2671 . G A 30.0349 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.738983;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=70;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:41:2:70:-5.5406,0,-2.40606 -chr_1 2686 . A G 28.1218 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=42.5;MQMR=36;NS=1;NUMALT=1;ODDS=0.861385;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=67;QR=39;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:39:2:67:-5.31237,0,-2.3529 -chr_1 2697 . G A 66.8365 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23789;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=104;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:104:-9.39261,-0.842345,0 -chr_1 2699 . G A 75.6507 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23781;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=103;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:103:-9.31979,-0.842311,0 -chr_1 2747 . C T 52.6764 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=5.92179;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=81;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=0;SAP=7.35324;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:81:-7.07265,-0.5718,0 -chr_1 3616 . C T 96.527 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=11.6962;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=8.55506;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=153;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:153:-10,-1.11336,0 -chr_1 3624 . A G 99.7577 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=11.6962;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=8.55532;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=158;QR=0;RO=0;RPP=11.6962;RPPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:158:-10,-1.11347,0 -chr_1 3630 . G A 119.888 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=13.8677;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=9.87182;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=191;QR=0;RO=0;RPP=13.8677;RPPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:191:-10,-1.38419,0 -chr_1 3657 . T C 146.729 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=9.87224;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=204;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=5;SAP=13.8677;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:204:-10,-1.38437,0 -chr_1 3681 . C T 141.607 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=8.80089;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.5;MQMR=0;NS=1;NUMALT=1;ODDS=11.1867;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=201;QR=0;RO=0;RPP=8.80089;RPPR=0;RUN=1;SAF=6;SAP=16.0391;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:201:-10,-1.65422,0 -chr_1 3746 . G A 143.027 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=42.8;MQMR=0;NS=1;NUMALT=1;ODDS=9.87133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=177;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=2;SAP=3.44459;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:177:-10,-1.38398,0 -chr_1 3766 . TGG TG 207.378 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1M1D1M;DP=7;DPB=4.66667;DPRA=0;EPP=3.32051;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.8571;MQMR=0;NS=1;NUMALT=1;ODDS=12.5052;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=267;QR=0;RO=0;RPP=3.32051;RPPR=0;RUN=1;SAF=1;SAP=10.7656;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=del;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:7:0:0:7:267:-10,-1.9258,0 -chr_1 3804 . C T 168.638 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=4.45795;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=42.1667;MQMR=0;NS=1;NUMALT=1;ODDS=11.188;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=213;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=1;SAP=8.80089;SAR=5;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:213:-10,-1.65476,0 -chr_1 3845 . G A 130.7 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=6.91895;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.8;MQMR=0;NS=1;NUMALT=1;ODDS=9.87163;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=184;QR=0;RO=0;RPP=13.8677;RPPR=0;RUN=1;SAF=1;SAP=6.91895;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:184:-10,-1.38411,0 -chr_1 3857 . G A 72.7109 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=0;NS=1;NUMALT=1;ODDS=7.23836;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=113;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=0;SAP=9.52472;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:113:-9.98004,-0.84255,0 -chr_1 4299 . C T 48.7928 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.73412;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=48;NS=1;NUMALT=1;ODDS=2.04069;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=100;QR=34;RO=1;RPP=9.52472;RPPR=5.18177;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:4:1:34:3:100:-7.69498,0,-2.01683 -chr_1 4311 . A G 138.174 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=6.91895;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40.2;MQMR=0;NS=1;NUMALT=1;ODDS=9.8711;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=179;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=3;SAP=3.44459;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:179:-10,-1.38387,0 -chr_1 4357 . C T 141.385 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=5;CIGAR=1X;DP=5;DPB=5;DPRA=0;EPP=3.44459;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=40.2;MQMR=0;NS=1;NUMALT=1;ODDS=9.87061;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=181;QR=0;RO=0;RPP=3.44459;RPPR=0;RUN=1;SAF=2;SAP=3.44459;SAR=3;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:5:0:0:5:181:-10,-1.38366,0 -chr_1 4372 . C T 57.8383 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.73412;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=40;MQMR=48;NS=1;NUMALT=1;ODDS=0.86483;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=40;RO=1;RPP=3.73412;RPPR=5.18177;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:4:1:40:3:110:-8.53351,0,-2.5275 -chr_1 4389 . C T 176.339 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=5.80219;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=45.4286;MQMR=48;NS=1;NUMALT=1;ODDS=6.11702;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=247;QR=37;RO=1;RPP=3.32051;RPPR=5.18177;RUN=1;SAF=3;SAP=3.32051;SAR=4;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:8:1:37:7:247:-10,0,-1.14959 -chr_1 4398 . T C 197.868 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=7;CIGAR=1X;DP=7;DPB=7;DPRA=0;EPP=5.80219;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=45.4286;MQMR=0;NS=1;NUMALT=1;ODDS=12.5039;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=243;QR=0;RO=0;RPP=3.32051;RPPR=0;RUN=1;SAF=3;SAP=3.32051;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:7:0:0:7:243:-10,-1.92523,0 -chr_1 4404 . T C 168.543 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=6;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=4.45795;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=46.3333;MQMR=0;NS=1;NUMALT=1;ODDS=11.1873;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=209;QR=0;RO=0;RPP=4.45795;RPPR=0;RUN=1;SAF=2;SAP=4.45795;SAR=4;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:6:0:0:6:209:-10,-1.65448,0 -chr_1 4475 . C T 81.0612 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=47;MQMR=0;NS=1;NUMALT=1;ODDS=7.2379;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-9.86084,-0.842352,0 -chr_1 4540 . C T 72.5101 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23698;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=101;QR=0;RO=0;RPP=9.52472;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:101:-9.00573,-0.841952,0 -chr_1 4580 . C T 81.3345 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=9.52472;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23817;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=119;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=1;SAP=3.73412;SAR=2;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:119:-9.88816,-0.842465,0 -chr_1 4611 . C G 51.9857 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=41.5;MQMR=0;NS=1;NUMALT=1;ODDS=5.92133;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=69;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=1;SAP=3.0103;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:69:-6.40152,-0.5716,0 -chr_1 4661 . A G 19.7502 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=43;NS=1;NUMALT=1;ODDS=0.834078;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=76;QR=35;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:35:2:76:-5.08162,0,-2.36476 -chr_1 4678 . G A 21.951 . AB=0.666667;ABP=3.73412;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.0103;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=43;NS=1;NUMALT=1;ODDS=0.136458;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=41;RO=1;RPP=3.0103;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=5.18177;SRR=1;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 0/1:3:1:41:2:68:-4.94794,0,-2.78626 -chr_1 4686 . C T 81.6957 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=3;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=3.73412;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=37.6667;MQMR=0;NS=1;NUMALT=1;ODDS=7.23731;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=110;QR=0;RO=0;RPP=3.73412;RPPR=0;RUN=1;SAF=2;SAP=3.73412;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:0:0:3:110:-9.44717,-0.842096,0 -chr_1 4699 . G A 103.379 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=4;CIGAR=1X;DP=4;DPB=4;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=36.75;MQMR=0;NS=1;NUMALT=1;ODDS=8.55324;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=140;QR=0;RO=0;RPP=5.18177;RPPR=0;RUN=1;SAF=3;SAP=5.18177;SAR=1;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:4:0:0:4:140:-10,-1.11256,0 -chr_1 4717 . C T 18.6085 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=3;DPB=3;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=35;MQMR=34;NS=1;NUMALT=1;ODDS=1.12012;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=40;RO=1;RPP=7.35324;RPPR=5.18177;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=1;SRP=5.18177;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:3:1:40:2:66:-4.87583,0,-2.24054 -chr_1 4727 . G A 43.4619 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=3.0103;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=32;MQMR=0;NS=1;NUMALT=1;ODDS=5.91984;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=66;QR=0;RO=0;RPP=3.0103;RPPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:66:-5.54913,-0.570955,0 -chr_1 4747 . C T 40.3421 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=2;CIGAR=1X;DP=2;DPB=2;DPRA=0;EPP=7.35324;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=34;MQMR=0;NS=1;NUMALT=1;ODDS=5.92045;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=68;QR=0;RO=0;RPP=7.35324;RPPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1 GT:DP:RO:QR:AO:QA:GL 1/1:2:0:0:2:68:-5.83919,-0.571218,0 -chr_1 3305168 . T A,G 280.615 . AB=0.75,0.25;ABP=9.52472,9.52472;AC=1,1;AF=0.5,0.5;AN=2;AO=9,3;CIGAR=1X,1X;DP=12;DPB=12;DPRA=0,0;EPP=9.04217,3.73412;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=4.632;PAIRED=1,1;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=319,107;QR=0;RO=0;RPP=9.04217,9.52472;RPPR=0;RUN=1,1;SAF=4,2;SAP=3.25157,3.73412;SAR=5,1;SRF=0;SRP=0;SRR=0;TYPE=snp,snp;technology.illumina=1,1 GT:DP:RO:QR:AO:QA:GL 1/2:12:0:0:9,3:319,107:-10,-8.89435,-6.43456,-10,0,-10 -chr_1 3305169 . T A,G 280.615 . AB=0.25,0.75;ABP=9.52472,9.52472;AC=1,1;AF=0.5,0.5;AN=2;AO=9,3;CIGAR=1X,1X;DP=12;DPB=12;DPRA=0,0;EPP=9.04217,3.73412;EPPR=0;GTI=0;LEN=1,1;MEANALT=2,2;MQM=60,60;MQMR=0;NS=1;NUMALT=2;ODDS=4.632;PAIRED=1,1;PAIREDR=0;PAO=0,0;PQA=0,0;PQR=0;PRO=0;QA=319,107;QR=0;RO=0;RPP=9.04217,9.52472;RPPR=0;RUN=1,1;SAF=4,2;SAP=3.25157,3.73412;SAR=5,1;SRF=0;SRP=0;SRR=0;TYPE=snp,snp;technology.illumina=1,1 GT:DP:RO:QR:AO:QA:GL 1/2:12:0:0:9,3:319,107:-10,-8.89435,-6.43456,-10,0,-10 diff -r a6b557df86db -r 3ca0f78f1102 test-data/chr17.VCF --- a/test-data/chr17.VCF Tue Dec 15 05:35:36 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,21 +0,0 @@ -##fileformat=VCFv4.1 -##fileDate=20140725 -##source=freeBayes v0.9.13-2-ga830efd -##reference=exmple.fsa -##phasing=none -##DetectedFormat=freebayes -##FILTER= -##FILTER= -##FILTER= -##FILTER= -##FILTER= -#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT V1 -chr_17 17 . A G 529.213 G_AF;G_DP AB=0.583333;ABP=5.18177;AC=1;AF=0.5;AN=2;AO=21;CIGAR=1X;DP=36;DPB=36;DPRA=0;EPP=3.1137;EPPR=3.15506;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=77.012;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=751;QR=535;RO=15;RPP=5.59539;RPPR=4.31318;RUN=1;SAF=11;SAP=3.1137;SAR=10;SRF=5;SRP=6.62942;SRR=10;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.58;G_DP=36;G_Base=G GT:DP:RO:QR:AO:QA:GL 0/1:36:15:535:21:751:-10,0,-10 -chr_17 37 . C G 1082.38 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=34;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=3.26577;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=48.0391;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1243;QR=0;RO=0;RPP=15.5282;RPPR=0;RUN=1;SAF=18;SAP=3.26577;SAR=16;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=34;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:34:0:0:34:1243:-10,-9.23017,0 -chr_17 40 . T T 825.518 G_AF AB=0;ABP=0;AC=2;AF=1;AN=2;AO=29;CIGAR=1X;DP=34;DPB=34;DPRA=0;EPP=6.67934;EPPR=13.8677;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=60;NS=1;NUMALT=1;ODDS=8.92992;PAIRED=1;PAIREDR=1;PAO=0;PQA=0;PQR=0;PRO=0;QA=1082;QR=178;RO=5;RPP=9.07545;RPPR=13.8677;RUN=1;SAF=13;SAP=3.68421;SAR=16;SRF=5;SRP=13.8677;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=0.85;G_DP=34;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:34:5:178:29:1082:-10,0,-6.82575 -chr_17 60 . A . 699.741 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=22;CIGAR=1X;DP=22;DPB=22;DPRA=0;EPP=17.2236;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=32.2544;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=823;QR=0;RO=0;RPP=9.32731;RPPR=0;RUN=1;SAF=12;SAP=3.40511;SAR=10;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=22;G_Base=G GT:DP:RO:QR:AO:QA:GL 1/1:22:0:0:22:823:-10,-5.98732,0 -chr_17 73 . T . 846.299 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=27;CIGAR=1X;DP=27;DPB=27;DPRA=0;EPP=16.6021;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=38.84;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1002;QR=0;RO=0;RPP=5.02092;RPPR=0;RUN=1;SAF=21;SAP=21.1059;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=27;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:27:0:0:27:1002:-10,-7.34226,0 -chr_17 81 . C T 764.464 . AB=0;ABP=0;AC=2;AF=1;AN=2;AO=25;CIGAR=1X;DP=25;DPB=25;DPRA=0;EPP=13.5202;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=36.1324;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=902;QR=0;RO=0;RPP=3.79203;RPPR=0;RUN=1;SAF=19;SAP=17.6895;SAR=6;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=25;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:25:0:0:25:902:-10,-6.76842,0 -chr_17 105 . C T 1154 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=37;CIGAR=1X;DP=37;DPB=37;DPRA=0;EPP=5.88603;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=52.0047;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1336;QR=0;RO=0;RPP=19.9713;RPPR=0;RUN=1;SAF=23;SAP=7.76406;SAR=14;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=37;G_Base=T GT:DP:RO:QR:AO:QA:GL 1/1:37:0:0:37:1336:-10,-10,0 -chr_17 112 . G A 1276.25 G_DP AB=0;ABP=0;AC=2;AF=1;AN=2;AO=40;CIGAR=1X;DP=40;DPB=40;DPRA=0;EPP=10.8276;EPPR=0;GTI=0;LEN=1;MEANALT=1;MQM=60;MQMR=0;NS=1;NUMALT=1;ODDS=55.9501;PAIRED=1;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1471;QR=0;RO=0;RPP=10.8276;RPPR=0;RUN=1;SAF=26;SAP=10.8276;SAR=14;SRF=0;SRP=0;SRR=0;TYPE=snp;technology.illumina=1;G_AN=2;G_AF=1.00;G_DP=40;G_Base=A GT:DP:RO:QR:AO:QA:GL 1/1:40:0:0:40:1471:-10,-10,0 - diff -r a6b557df86db -r 3ca0f78f1102 test-data/chr17.fa --- a/test-data/chr17.fa Tue Dec 15 05:35:36 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,3 +0,0 @@ ->chr_17 -ccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaa -TACGCGCGCGCCTAACCCTACGACTTTAACCTACTCTAAACTCTCCTACTAGTACGTCTT diff -r a6b557df86db -r 3ca0f78f1102 tool_dependencies.xml --- a/tool_dependencies.xml Tue Dec 15 05:35:36 2015 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,19 +0,0 @@ - - - - - - https://urgi.versailles.inra.fr/download/gandalf/VCFtools-1.2.tar.gz - python setup_VCFtools.py install - - . - $INSTALL_DIR - - - $INSTALL_DIR - $INSTALL_DIR/bin - - - - -