jvarkit
VCFTabixml
annotate a value from a vcf+xml file
DEPRECATED
ugly tool, please don’t use it
Usage
Usage: java -jar dist/vcftabixml.jar [options] Files
Usage: vcftabixml [options] Files
Options:
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --output
Output file. Optional . Default: stdout
--version
print version and exit
* -B
BED file indexed with tabix. The 4th column *is* a XML string.)
* -F
file containing extra INFO headers line to add version: 4.1
* -xsl
x xslt-stylesheet. REQUIRED. Should produce a valid set of INFO field.
Keywords
- vcf
- xml
Compilation
Requirements / Dependencies
- java compiler SDK 11. Please check that this java is in the
${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
Download and Compile
$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew vcftabixml
The java jar file will be installed in the dist directory.
Source code
Contribute
- Issue Tracker: http://github.com/lindenb/jvarkit/issues
- Source Code: http://github.com/lindenb/jvarkit
License
The project is licensed under the MIT license.
Citing
Should you cite vcftabixml ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030
4th column of the BED indexed with TABIX is a XML string.
It will be processed with the xslt-stylesheet and should procuce a xml result
Example
The header of the tabix-index BED+XML file:
1 69427 69428 <snpList><positionString>1:69428</positionString><chrPosition>69428</chrPosition><alleles>G/T</alleles><ua..
1 69475 69476 <snpList><positionString>1:69476</positionString><chrPosition>69476</chrPosition><alleles>C/T</alleles><ua..
1 69495 69496 <snpList><positionString>1:69496</positionString><chrPosition>69496</chrPosition><alleles>A/G</alleles><ua..
1 69510 69511 <snpList><positionString>1:69511</positionString><chrPosition>69511</chrPosition><alleles>G/A</alleles><ua...
1 69589 69590 <snpList><positionString>1:69590</positionString><chrPosition>69590</chrPosition><alleles>A/T</alleles><ua...
1 69593 69594 <snpList><positionString>1:69594</positionString><chrPosition>69594</chrPosition><alleles>C/T</alleles><ua..
1 69619 69620 <snpList><positionString>1:69620</positionString><chrPosition>69620</chrPosition><alleles>T/TA</alleles><u...
1 69744 69745 <snpList><positionString>1:69745</positionString><chrPosition>69745</chrPosition><alleles>CA/C</alleles><u..
1 69760 69761 <snpList><positionString>1:69761</positionString><chrPosition>69761</chrPosition><alleles>T/A</alleles><ua...
1 801942 801943 <snpList><positionString>1:801943</positionString><chrPosition>801943</chrPosition><alleles>T/C</alleles...
(...)
The content of the tags.txt file:
##INFO=<ID=EVS_AAMAF,Number=1,Type=String,Description="EVS_AAMAF from EVS">
##INFO=<ID=EVS_AVGSAMPLEREADDEPTH,Number=1,Type=String,Description="EVS_AVGSAMPLEREADDEPTH from EVS">
##INFO=<ID=EVS_CLINICALLINK,Number=1,Type=String,Description="EVS_CLINICALLINK from EVS">
##INFO=<ID=EVS_CONFLICTALT,Number=1,Type=String,Description="EVS_CONFLICTALT from EVS">
##INFO=<ID=EVS_CONSERVATIONSCOREGERP,Number=1,Type=String,Description="EVS_CONSERVATIONSCOREGERP from EVS">
##INFO=<ID=EVS_CONSERVATIONSCORE,Number=1,Type=String,Description="EVS_CONSERVATIONSCORE from EVS">
##INFO=<ID=EVS_GENELIST,Number=1,Type=String,Description="EVS_GENELIST from EVS">
##INFO=<ID=EVS_GWASPUBMEDIDS,Number=1,Type=String,Description="EVS_GWASPUBMEDIDS from EVS">
##INFO=<ID=EVS_ONEXOMECHIP,Number=1,Type=String,Description="EVS_ONEXOMECHIP from EVS">
##INFO=<ID=EVS_RSIDS,Number=1,Type=String,Description="EVS_RSIDS from EVS">
##INFO=<ID=EVS_TOTALMAF,Number=1,Type=String,Description="EVS_TOTALMAF from EVS">
##INFO=<ID=EVS_UAMAF,Number=1,Type=String,Description="EVS_UAMAF from EVS">
The XSLT file:
<?xml version="1.0" encoding="ISO-8859-1"?>
<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform" version="1.0">
<xsl:output method="xml"/>
<xsl:param name="vcfchrom"/>
<xsl:param name="vcfpos"/>
<xsl:param name="vcfref"/>
<xsl:param name="vcfalt"/>
<xsl:template match="/">
<properties>
<xsl:apply-templates select="evsData|snpList"/>
</properties>
</xsl:template>
<xsl:template match="evsData">
<xsl:a*
* @author lindenb
*pply-templates select="snpList"/>
</xsl:template>
<xsl:template match="snpList">
<xsl:choose>
<xsl:when test="chromosome=$vcfchrom and chrPosition=$vcfpos and refAllele=$vcfref">
<xsl:apply-templates select="clinicalLink|rsIds|uaMAF|aaMAF|totalMAF|avgSampleReadDepth|geneList|conservationScore|conservationScoreGERP|gwasPubmedIds|onExomeChip|gwasPubmedIds"/>
<xsl:if test="altAlleles!=$vcfalt">
<entry key="EVS_CONFLICTALT">
<xsl:value-of select="altAlleles"/>
</entry>
</xsl:if>
</xsl:when>
<xsl:otherwise/>
</xsl:choose>
</xsl:template>
<xsl:template match="clinicalLink|rsIds|uaMAF|aaMAF|totalMAF|avgSampleReadDepth|geneList|conservationScore|conservationScoreGERP|onExomeChip|gwasPubmedIds">
<xsl:if test="string-length(normalize-space(text()))>0">
<entry>
<xsl:attribute name="key"><xsl:value-of select="concat('EVS_',translate(name(.),'abcdefghijklmnopqrstuvwxyz','ABCDEFGHIJKLMNOPQRSTUVWXYZ'))"/></xsl:attribute>
<xsl:value-of select="text()"/>
</entry>
</xsl:if>
</xsl:template>
</xsl:stylesheet>
Running:
java -jar dist/vcftabixml.jar \
IN=input.vcf.gz \
XSL=evs2vcf.xsl \
BEDFILE=evs.data.gz \
TAGS=tags.txt | grep -v "##" | head
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT U0925
A 613326 . G A 182 . AC1=1;AF1=0.5;DP=327;DP4=0,147,0,178;FQ=163;MQ=47;PV4=1,0.21,1.2e-35,1;RPB=6.999638e+00;VDB=8.105711e-05 GT:PL:DP:GQ 0/1:212,0,190:325:99
A 614565 . A G 222 . AC1=2;AF1=1;DP=910;DP4=0,1,71,836;EVS_AAMAF=23.2659;EVS_AVGSAMPLEREADDEPTH=70;EVS_CLINICALLINK=unknown;EVS_CONSERVATIONSCORE=0.0;EVS_CONSERVATIONSCOREGERP=-3.5;EVS_GENELIST=KCNAB2;EVS_GWASPUBMEDIDS=unknown;EVS_ONEXOMECHIP=false;EVS_RSIDS=rs26;EVS_TOTALMAF=30.5519;EVS_UAMAF=33.7209;FQ=-282;MQ=41;PV4=1,0.26,0.032,1;RPB=1.705346e+00;VDB=1.656917e-35 GT:PL:DP:GQ 1/1:255,255,0:908:99
A 614379 . C T 225 . AC1=1;AF1=0.5;DP=979;DP4=33,440,37,456;EVS_AAMAF=2.8179;EVS_AVGSAMPLEREADDEPTH=59;EVS_CLINICALLINK=unknown;EVS_CONSERVATIONSCORE=0.0;EVS_CONSERVATIONSCOREGERP=-4.7;EVS_GENELIST=KCNAB2;EVS_GWASPUBMEDIDS=unknown;EVS_ONEXOMECHIP=false;EVS_RSIDS=rs249;EVS_TOTALMAF=8.8261;EVS_UAMAF=11.4393;FQ=225;MQ=42;PV4=0.8,1,3.8e-152,1;RPB=1.317662e+01;VDB=3.857882e-21 GT:PL:DP:GQ 0/1:255,0,255:966:99
A 614565 . T G 222 . AC1=2;AF1=1;DP=209;DP4=0,0,0,187;FQ=-282;MQ=46;VDB=2.410569e-12 GT:PL:DP:GQ 1/1:255,255,0:187:99
A 614953 . C T 225 . AC1=1;AF1=0.5;DP=810;DP4=197,214,194,195;EVS_AAMAF=2.4603;EVS_AVGSAMPLEREADDEPTH=45;EVS_CLINICALLINK=unknown;EVS_CONSERVATIONSCORE=0.0;EVS_CONSERVATIONSCOREGERP=-3.1;EVS_GENELIST=KCNAB2;EVS_GWASPUBMEDIDS=unknown;EVS_ONEXOMECHIP=false;EVS_RSIDS=rs733;EVS_TOTALMAF=7.0506;EVS_UAMAF=9.4205;FQ=225;MQ=47;PV4=0.62,1,9.2e-58,0.015;RPB=4.560133e+00;VDB=6.880316e-03 GT:PL:DP:GQ 0/1:255,0,255:800:99
A 614922 . G A 130 . AC1=1;AF1=0.5;DP=183;DP4=0,94,0,86;EVS_AAMAF=2.3053;EVS_AVGSAMPLEREADDEPTH=43;EVS_CLINICALLINK=unknown;EVS_CONSERVATIONSCORE=0.0;EVS_CONSERVATIONSCOREGERP=-3.0;EVS_GENELIST=KCNAB2;EVS_GWASPUBMEDIDS=unknown;EVS_ONEXOMECHIP=false;EVS_RSIDS=rs202;EVS_TOTALMAF=7.1215;EVS_UAMAF=9.6386;FQ=133;MQ=44;PV4=1,0.0065,3.7e-51,1;RPB=3.500959e+00;VDB=9.915205e-29 GT:PL:DP:GQ 0/1:160,0,184:180:99
A 614986 . G C 188 . AC1=2;AF1=1;DP=176;DP4=0,0,0,175;FQ=-282;MQ=46;VDB=0.000000e+00 GT:PL:DP:GQ 1/1:221,255,0:175:99
A 615009 . T A 125 . AC1=1;AF1=0.5;DP=103;DP4=45,0,56,0;FQ=120;MQ=45;PV4=1,0.14,2.8e-19,1;RPB=1.520268e+00;VDB=1.539079e-06 GT:PL:DP:GQ 0/1:155,0,148:101:99
A 615037 . C T 161 . AC1=1;AF1=0.5;DP=353;DP4=0,164,0,165;FQ=110;MQ=48;PV4=1,1,1.1e-23,1;RPB=5.549816e+00;VDB=1.486773e-11 GT:PL:DP:GQ 0/1:191,0,137:329:99