Olorin

Olorin is an interactive filtering tool for next generation sequencing data coming from the study of large complex disease pedigrees.

Olorin, is a tool which integrates gene flow output from Merlin and next generation sequencing data. Users can interactively filter and prioritize variants based on haplotype sharing across different sets of selected individuals and allele frequency in reference datasets.

[James Morris]

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System requirements

Olorin is written in Java and will work on any platform with Java 1.6 or later.

FAQ

Loading data

Why can Olorin not find my VCF index?
Where a VCF file is named in the following way: example.vcf.gz
Olorin expects the VCF index file to be named: example.vcf.gz.tbi
What should I do if Olorin has problems fetching variants from the VCF?
First test that your VCF file was successfully indexed, you can do this on the command line using tabix and the following command: 
tabix example.vcf.gz 1:0-1000000
This command should print out all the variants in the first megabase of chromosome one in your VCF. Try this command on a region of the genome that you know contains variants, if this does not work then try indexing your VCF again. If this does not help then you should also check that your VCF is in a valid format. You can check if your VCF is valid using VCFtools.
What options does MERLIN require to produce output for Olorin?
Olorin requires the .flow files to be in the horizontal format for outputting haplotypes, MERLIN should therefore be run using the --horizontal flag.

Display

How can I make the genome wide ideogram plot larger?
You can use the clickable expanding arrows found in each of the panel dividers allow each of the panels to be fully expanded to the full X or Y dimension of the Olorin window.
How can I identify the sample name of a node in the pedigree?
Holding the pointer over the point of interest will show which sample corresponds to that node.

Other

What do I do if Olorin runs out of memory?
If Olorin needs more memory to load a data set then users can launch the program with additional memory from the command line by issuing the following command (increasing the -Xmx value as necessary): 
java -Xmx1024m -jar Olorin.jar

Publications

  • Olorin: combining gene flow with exome sequencing in large family studies of complex disease.

    Morris JA and Barrett JC

    Bioinformatics (Oxford, England) 2012;28;24;3320-1

    PUBMED: 23052039; PMC: 3519455; DOI: 10.1093/bioinformatics/bts609

Contact

Join our Olorin mailing list to stay informed about updates and new releases.

For questions or comments, please contact James Morris or Jeff Barrett.

* quick link - http://q.sanger.ac.uk/olorin