Genome Coordinates Converter

Java wrapper for performing various conversions between common identifiers.

Requirements

• Java 8
• Python
• hgvs python package

Converters:

- Liftover
- HGVS to Genomic Coordinates

LiftOver

liftOvers on genomic coordinates. The wrapper provides easy to use methods for converting genomic coordinates from one build version to another. Additionally, it is pre-configured to offer support for the most common conversions.

Chain Files

LiftOvers can be performed easily by either using the predefined liftovers, or by supplying a custom chain file. Chain files are written in the Chain Format from UCSC. A large number of chainfiles are publicly available to download here,

Basic Usage

    try {
        LiftOver intervalLiftOver = UCSCLiftOver.hg19ToHg38();
        Interval newInterval = intervalLiftOver.liftOver("chr1",743267,743268);
    } catch(LiftOverException e){
        e.printStackTrace();
    } catch(IOException e){
        e.printStackTrace();
        
    }

Using a Custom Chain File

   try {
       String path = "/path/to/customChainFile";
       String from = "mm9";
       String to = "mm10";
    
       ChainFile chainFile = new UCSCChainFile(path, from, to);
       LiftOver intervalLiftOver = new UCSCLiftOver(chainFile);
       Interval newInterval = intervalLiftOver.liftOver("chr1",7724,8662);
   } catch(LiftOverException e){
        e.printStackTrace();
   } catch(IOException e){
        e.printStackTrace();
   }
   

Built in LiftOvers

Several liftovers have been included

From	To
hg17	hg18
hg17	hg19
hg18	hg17
hg18	hg19
hg18	hg38
hg19	hg17
hg19	hg18
hg19	hg38
hg38	hg19

HGVS to Genomic Coordinate Converter

The HGVS to genomic coordinate converter offers a thin wrapper around the hgvs python package for your java project. It will take any valid HGVS and convert it to genomic positions.

Installing HGVS

In order to use this pacakage you must first install both python and HGVS on the computer you will be running this.

Use pip to install hgvs:

pip install hgvs

If you are using OSX and run into a problem while installing hgvs, you may need to install supporting postgresql libraries:

brew install postgresql

Basic Usage

try { 
    String hgvs = "NM_182763.2:c.688+403C>T"
    GenomeInterval interval = HGVSConverter.hgvsToGenomic(hgvs);
} catch(HGVSException e){
    e.printStackTrace();
}