Command-line application to generate a report for any VCF (Variant Call Format) file based on a report template.
- Java 17
usage: java -jar vcf-report.jar -i <arg> [-m <arg>] [-o <arg>] [-f] [-t <arg>] [-pb
<arg>] [-pd <arg>] [-ph <arg>] [-ms <arg>] [-r <arg>]
[-g <arg>] [-c <arg>] [-dt <arg>] [-d]
-i,--input <arg> Input VCF file (.vcf or .vcf.gz).
-m,--metadata <arg> VCF metadata file (.json).
-o,--output <arg> Output report file (.html).
-f,--force Override the output file if it already
exists.
-t,--template <arg> Report template file (.html).
-pb,--probands <arg> Comma-separated list of proband names.
-pd,--pedigree <arg> Comma-separated list of pedigree files
(.ped).
-ph,--phenotypes <arg> Comma-separated list of sample-phenotypes
(e.g. HP:123 or HP:123;HP:234 or
sample0/HP:123,sample1/HP:234). Phenotypes
are CURIE formatted (prefix:reference) and
separated by a semicolon.
-ms,--max_samples <arg> Integer stating the maximum number of samples
to be available in the report. Default: 100
-r,--reference <arg> Reference sequence file (.fasta.gz, .fna.gz,
.fa.gz, .ffn.gz, .faa.gz or .frn.gz).
-g,--genes <arg> Genes file to be used as reference track in the
genome browser, UCSC NCBI RefSeq GFF file
(gff.gz or gff3.gz).
-c,--cram <arg> Comma-separated list of sample-bam files
(e.g.
sample0=/path/to/0.cram,sample1=/path/to/1.cram
).
-dt,--decision_tree <arg> Decision tree file as used in
vip-decision-tree (.json).
-d,--debug Enable debug mode (additional logging and
pretty printed report).
usage: java -jar vcf-report.jar -v
-v,--version Print version.
*: CURIE
java -jar vcf-report.jar -i my.vcf.gz -m metadata.json -t my-template.html
java -jar vcf-report.jar -i my.vcf.gz -m metadata.json -o my-report.html -t my-template.html
java -jar vcf-report.jar -i my.vcf.gz -m metadata.json -o my-report.html -t my-template.html
java -jar vcf-report.jar -i my.vcf.gz -m metadata.json -o my-report.html -t my-template.html -pb sample0,sample1 -pd my.ped,my_other.ped
java -jar vcf-report.jar -i my.vcf.gz -m metadata.json -o my-report.html -t my-template.html -pb sample0,sample1 -pd my.ped,my_other.ped
java -jar vcf-report.jar -i my.vcf.gz -m metadata.json -o my-report.html -t my-template.html -pb sample0,sample1 -pd my.ped,my_other.ped -ph HP:0000001;HP:0000002
java -jar vcf-report.jar -i my.vcf.gz -m metadata.json -o my-report.html -t my-template.html -pb sample0,sample1 -pd my.ped,my_other.ped -ph sampleId1/HP:0000001;HP:0000002,sampleId2/HP:0000001
java -jar vcf-report.jar -i my.vcf.gz -m metadata.json -o my-report.html -t my-template.html -pb sample0,sample1 -pd my.ped,my_other.ped -ph sampleId1/HP:0000001;HP:0000002,sampleId2/HP:0000001 -ms 10
java -jar vcf-report.jar -v
You report might contain more data than your web browser can handle. Try reducing the number of VCF records, setting a lower value for --max_samples and reducing alignment data in .cram files.
In case of long-read alignment sequences try removing --cram from the argument list.
Generate a personal access token in GitHub with at least the scope "read:packages".
Then add a settings.xml to your Maven .m2 folder, or edit it if you already have one. It should contain the following:
<?xml version="1.0"?>
<settings xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.0.0 http://maven.apache.org/xsd/settings-1.0.0.xsd" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://maven.apache.org/SETTINGS/1.0.0">
<activeProfiles>
<activeProfile>github</activeProfile>
</activeProfiles>
<profiles>
<profile>
<id>github</id>
<repositories>
<repository>
<id>central</id>
<url>https://repo1.maven.org/maven2</url>
</repository>
<repository>
<id>github</id>
<url>https://maven.pkg.github.com/molgenis/vip-utils</url>
<snapshots>
<enabled>true</enabled>
</snapshots>
</repository>
</repositories>
</profile>
</profiles>
<servers>
<server>
<id>github</id>
<username>[YOUR VIP USERNAME]</username>
<password>[YOUR PERSONAL ACCESS TOKEN]</password>
</server>
</servers>
</settings>
The report generator transforms the input data to a JavaScript object (window.api) that is injected into the report template at the end of the head tag.
Consider the following template:
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<title>Report</title>
</head>
<body>
<div id="report"></div>
<script>
document.getElementById("report").innerHTML = JSON.stringify(api.data)
</script>
</body>
</html>The resulting report after rendering the template using input data will look like:
<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<title>Report</title>
<script>
window.api = {...}
</script>
</head>
<body>
<div id="report"></div>
<script>
document.getElementById("report").innerHTML = JSON.stringify(api)
</script>
</body>
</html>The format of the variant report data is described in the org.molgenis.vcf.report.model Java
classes.
The format of the phenotype data is described here: Phenopackets_Person
The format of the sample data is described here: Phenopacket Please note that only a subset of PhenotypicFeature fields is returned.
"phenotypes": {
"items": [
{
"subject": {
"id": "SampleId123"
},
"phenotypicFeaturesCount": 2,
"phenotypicFeaturesList": [
{
"type": {
"id": "HP:123456",
"label": "HP:123456"
}
},
{
"type": {
"id": "HP:234567",
"label": "HP:234567"
}
}
]
}