jvarkit

VCFTabixml

Last commit

annotate a value from a vcf+xml file

Usage

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

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

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/vcftabixml/VCFTabixml.java

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 value1</property>values1</properies> INFO fields. Carriage returns will be removed." Parameters to be passed to the stylesheet: vcfchrom (string) vcfpos(int) vcfref(string) vcfalt(string).

Example

The header of the tabix-index BED+XML file:

69427	69428	<snpList><positionString>1:69428</positionString><chrPosition>69428</chrPosition><alleles>G/T</alleles><ua..
69475	69476	<snpList><positionString>1:69476</positionString><chrPosition>69476</chrPosition><alleles>C/T</alleles><ua..
69495	69496	<snpList><positionString>1:69496</positionString><chrPosition>69496</chrPosition><alleles>A/G</alleles><ua..
69510	69511	<snpList><positionString>1:69511</positionString><chrPosition>69511</chrPosition><alleles>G/A</alleles><ua...
69589	69590	<snpList><positionString>1:69590</positionString><chrPosition>69590</chrPosition><alleles>A/T</alleles><ua...
69593	69594	<snpList><positionString>1:69594</positionString><chrPosition>69594</chrPosition><alleles>C/T</alleles><ua..
69619	69620	<snpList><positionString>1:69620</positionString><chrPosition>69620</chrPosition><alleles>T/TA</alleles><u...
69744	69745	<snpList><positionString>1:69745</positionString><chrPosition>69745</chrPosition><alleles>CA/C</alleles><u..
69760	69761	<snpList><positionString>1:69761</positionString><chrPosition>69761</chrPosition><alleles>T/A</alleles><ua...
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()))&gt;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

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