VcfRegistryWeb

##Motivation

CGI/Web tool printing all the variants at a given position for a collection of tabix-ed VCF files.

output example:

CHROM	POS	ID	REF	QUAL	Sample	Alleles	DP	GQ	File
22	11905981	rs86876	A	3133	SAMPLE_273	A/G	211	99	/path/to/SAMPLE_273_variations.gatk.annotations.vcf.gz
22	11905981	rs86876	A	143	SAMPLE_273	G/G	221	99	/path/to/SAMPLE_273_variations.samtools.annotations.vcf.gz
22	11905981	rs86876	A	2455	SAMPLE_324	A/G	165	99	/path/to/SAMPLE_324_variations.gatk.annotations.vcf.gz
22	11905981	rs86876	A	118	SAMPLE_324	G/G	167	99	/path/to/SAMPLE_324_variations.samtools.annotations.vcf.gz
22	11905981	rs86876	A	6398	SAMPLE_016	A/G	462	99	/path/to/SAMPLE_016_variations.gatk.annotations.vcf.gz
22	11905981	rs86876	A	133	SAMPLE_016	A/G	482	99	/path/to/SAMPLE_016_variations.samtools.annotations.vcf.gz
(...)	(...)		(...)	(...)	(...)	(...)	(...)	(...)	(...)

##Compilation/Installation

Create a Preference file.

create/update a java preferences file with the following key/example:

<?xml version="1.0"?>
<!DOCTYPE preferences SYSTEM "http://java.sun.com/dtd/preferences.dtd">
<preferences EXTERNAL_XML_VERSION="1.0">
  <root type="user">
    <map>
      <entry key="vcf.registry.group.file" value="/var/www/cgi-bin/vcfregistry.tsv"/>
    </map>
  </root>
</preferences>

here /var/www/cgi-bin/vcfregistry.tsv is a tab delimited file containing the path to some collections of VCFs (path/Title):

$ cat vcfregistry.tsv
/var/www/cgi-bin/vcfregistry1.tsv       Collection1
/var/www/cgi-bin/vcfregistry2.tsv       Collection2
/var/www/cgi-bin/vcfregistry3.tsv       Collection3

A collection file contains a list of VCF indexed with tabix:

$ head /var/www/cgi-bin/vcfregistry1.tsv 
/commun/data/projects/TEST/align/Samples/SAMPLE_73/VCF/SAMPLE_73_variations.gatk.annotations.vcf.gz
/commun/data/projects/TEST/align/Samples/SAMPLE_73/VCF/SAMPLE_73_variations.samtools.annotations.vcf.gz
/commun/data/projects/TEST/align/Samples/SAMPLE_72/VCF/SAMPLE_72_variations.gatk.annotations.vcf.gz
/commun/data/projects/TEST/align/Samples/SAMPLE_72/VCF/SAMPLE_72_variations.samtools.annotations.vcf.gz
/commun/data/projects/TEST/align/Samples/SAMPLE_71/VCF/SAMPLE_71_variations.gatk.annotations.vcf.gz
/commun/data/projects/TEST/align/Samples/SAMPLE_71/VCF/SAMPLE_71_variations.samtools.annotations.vcf.gz
/commun/data/projects/TEST/align/Samples/SAMPLE_24/VCF/SAMPLE_24_variations.gatk.annotations.vcf.gz
/commun/data/projects/TEST/align/Samples/SAMPLE_24/VCF/SAMPLE_24_variations.samtools.annotations.vcf.gz
/commun/data/projects/TEST/align/Samples/SAMPLE_16/VCF/SAMPLE_16_variations.gatk.annotations.vcf.gz
/commun/data/projects/TEST/align/Samples/SAMPLE_16/VCF/SAMPLE_16_variations.samtools.annotations.vcf.gz

Compile the program

See also Compilation.

Important : the JAR/library files of picard should be visible from the CGI-bin. The path defined in the build.properties should be absolute.

$ ant vcfregistry.cgi

It creates a jar file (vcfregistry.jar) and an executable shell script (vcfregistry.cgi) in the 'dist' folder. Both should be moved in the cgi-bin script of your server:

$ sudo mv dist/vcfregistry* /var/www/cgi-bin/

If needed, edit the script tviewweb.cgi and change the JVM property Dprefs.file.xml= to the correct place of your xml preference file.

java (...) -Dprefs.file.xml=/var/www/cgi-bin/prefs.xml (...)