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.

About

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System requirements

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

Further information

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

Contact

If you need help or have any queries, please contact us using the details below.

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


Sanger Institute Contributors

Previous contributors

Photo of Dr Jeffrey Barrett

Dr Jeffrey Barrett

Former Director of Open Targets & Former Senior Group Leader

Photo of James Morris

James Morris

Research Assistant