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EVS2BED
Downloads the content of the exome variant server to a bed file chrom/start/end/xml
bioinformatics, vcf, bed, evs Downloads the content of the exome variant server ( http://evs.gs.washington.edu/EVS/ ) to a bed file chrom/start/end/xml Download and Compilesvn checkout http://jvarkit.googlecode.com/svn/trunk/ jvarkit cd jvarkit edit the file build.properies and add the path to the picard API: picard.jar=/path/to/picard-tools-1.79/picard-1.79.jar sam.jar=/path/to/picard-tools-1.79/sam-1.79.jar and compile: ant vcftabixml UsageUsage: java -jar evs2bed.jar > evs.bed Options-S (int) download using a step of 'S' bases. OPTIONAL. -L (int) limit to 'N' records for testing. OPTIONAL. --proxyHost <string> optional --proxyPort <string> optional ExampleDownload and index the data with tabix: java -jar dist/evs2bed.jar -L 10 | LC_ALL=C sort -k1,1 -k2,2n -k3,3n -k4,4 -u |\ /path/totabix-0.2.6/bgzip -c > test.bed.gz /path/totabix-0.2.6/tabix -p bed -f test.bed.gz $ gunzip -c test.bed.gz | cut -c 1-500 | fold -w 80 1 69427 69428 <snpList><positionString>1:69428</positionString><chrPos ition>69428</chrPosition><alleles>G/T</alleles><uaAlleleCounts>G=313/T=6535</uaA lleleCounts><aaAlleleCounts>G=14/T=3808</aaAlleleCounts><totalAlleleCounts>G=327 /T=10343</totalAlleleCounts><uaMAF>4.5707</uaMAF><aaMAF>0.3663</aaMAF><totalMAF> 3.0647</totalMAF><avgSampleReadDepth>110</avgSampleReadDepth><geneList>OR4F5</ge neList><snpFunction><chromosome>1</chromosome><position>69428</position><conserv ationScore>1.0</conservationSc 1 69475 69476 <snpList><positionString>1:69476</positionString><chrPos ition>69476</chrPosition><alleles>C/T</alleles><uaAlleleCounts>C=2/T=7020</uaAll eleCounts><aaAlleleCounts>C=0/T=3908</aaAlleleCounts><totalAlleleCounts>C=2/T=10 928</totalAlleleCounts><uaMAF>0.0285</uaMAF><aaMAF>0.0</aaMAF><totalMAF>0.0183</ totalMAF><avgSampleReadDepth>123</avgSampleReadDepth><geneList>OR4F5</geneList>< snpFunction><chromosome>1</chromosome><position>69476</position><conservationSco re>0.6</conservationScore><con 1 69495 69496 <snpList><positionString>1:69496</positionString><chrPos ition>69496</chrPosition><alleles>A/G</alleles><uaAlleleCounts>A=2/G=6764</uaAll eleCounts><aaAlleleCounts>A=23/G=3785</aaAlleleCounts><totalAlleleCounts>A=25/G= 10549</totalAlleleCounts><uaMAF>0.0296</uaMAF><aaMAF>0.604</aaMAF><totalMAF>0.23 64</totalMAF><avgSampleReadDepth>91</avgSampleReadDepth><geneList>OR4F5</geneLis t><snpFunction><chromosome>1</chromosome><position>69496</position><conservation Score>0.5</conservationScore>< 1 69510 69511 <snpList><positionString>1:69511</positionString><chrPos ition>69511</chrPosition><alleles>G/A</alleles><uaAlleleCounts>G=5337/A=677</uaA lleleCounts><aaAlleleCounts>G=1937/A=1623</aaAlleleCounts><totalAlleleCounts>G=7 274/A=2300</totalAlleleCounts><uaMAF>11.2571</uaMAF><aaMAF>45.5899</aaMAF><total MAF>24.0234</totalMAF><avgSampleReadDepth>69</avgSampleReadDepth><geneList>OR4F5 </geneList><snpFunction><chromosome>1</chromosome><position>69511</position><con servationScore>1.0</conservati 1 69589 69590 <snpList><positionString>1:69590</positionString><chrPos ition>69590</chrPosition><alleles>A/T</alleles><uaAlleleCounts>A=0/T=6214</uaAll eleCounts><aaAlleleCounts>A=1/T=3555</aaAlleleCounts><totalAlleleCounts>A=1/T=97 69</totalAlleleCounts><uaMAF>0.0</uaMAF><aaMAF>0.0281</aaMAF><totalMAF>0.0102</t otalMAF><avgSampleReadDepth>119</avgSampleReadDepth><geneList>OR4F5</geneList><s npFunction><chromosome>1</chromosome><position>69590</position><conservationScor e>0.8</conservationScore><cons 1 69593 69594 <snpList><positionString>1:69594</positionString><chrPos ition>69594</chrPosition><alleles>C/T</alleles><uaAlleleCounts>C=2/T=6190</uaAll eleCounts><aaAlleleCounts>C=0/T=3548</aaAlleleCounts><totalAlleleCounts>C=2/T=97 38</totalAlleleCounts><uaMAF>0.0323</uaMAF><aaMAF>0.0</aaMAF><totalMAF>0.0205</t otalMAF><avgSampleReadDepth>109</avgSampleReadDepth><geneList>OR4F5</geneList><s npFunction><chromosome>1</chromosome><position>69594</position><conservationScor e>0.8</conservationScore><cons 1 69619 69620 <snpList><positionString>1:69620</positionString><chrPos ition>69620</chrPosition><alleles>T/TA</alleles><uaAlleleCounts>A1=2/R=4694</uaA lleleCounts><aaAlleleCounts>A1=0/R=2954</aaAlleleCounts><totalAlleleCounts>A1=2/ R=7648</totalAlleleCounts><uaMAF>0.0426</uaMAF><aaMAF>0.0</aaMAF><totalMAF>0.026 1</totalMAF><avgSampleReadDepth>56</avgSampleReadDepth><geneList>OR4F5</geneList ><snpFunction><chromosome>1</chromosome><position>69620</position><conservationS core>0.7</conservationScore><c 1 69744 69745 <snpList><positionString>1:69745</positionString><chrPos ition>69745</chrPosition><alleles>CA/C</alleles><uaAlleleCounts>A1=4/R=4254</uaA lleleCounts><aaAlleleCounts>A1=0/R=2716</aaAlleleCounts><totalAlleleCounts>A1=4/ R=6970</totalAlleleCounts><uaMAF>0.0939</uaMAF><aaMAF>0.0</aaMAF><totalMAF>0.057 4</totalMAF><avgSampleReadDepth>10</avgSampleReadDepth><geneList>OR4F5</geneList ><snpFunction><chromosome>1</chromosome><position>69745</position><conservationS core>0.9</conservationScore><c 1 69760 69761 <snpList><positionString>1:69761</positionString><chrPos ition>69761</chrPosition><alleles>T/A</alleles><uaAlleleCounts>T=645/A=4093</uaA lleleCounts><aaAlleleCounts>T=62/A=2840</aaAlleleCounts><totalAlleleCounts>T=707 /A=6933</totalAlleleCounts><uaMAF>13.6133</uaMAF><aaMAF>2.1365</aaMAF><totalMAF> 9.2539</totalMAF><avgSampleReadDepth>8</avgSampleReadDepth><geneList>OR4F5</gene List><snpFunction><chromosome>1</chromosome><position>69761</position><conservat ionScore>0.1</conservationScor |