tkonopka / geneticthesaurus

Thesaurus for genetic variants

GeneticThesaurus

GeneticThesaurus is designed for analysis of genetic variation in repetitive regions. It contains programs that build a table describing genomic regions with similar sequence. It also provides tools that use the resource to annotate variants.

To run the GeneticThesaurus, you will need java (version 6 or above). Execute the program using the command

java -jar GeneticThesaurus.jar

You may need to provide the java virtual machine access to a larger pool of memory than is allowed by default. In such situations, additionally use the -Xmx flag. For example, to provide 24GB of heap memory, use

java -Xmx24g -jar GeneticThesaurus.jar

Development and Distribution

The project is developed on github.com and distributed on sourceforge.net under the name "GeneticThesaurus".

Documentation

Usage information is available on the wiki pages at www.sourceforge.net.

Authors

GeneticThesaurus is described in an academic publication. If you find GeneticThesaurus useful, please cite

C. Kerzendorfer, T. Konopka, S. Nijman. "A thesaurus of genetic variation for interrogation of repetitive genomic regions" Nucleic Acids Research

T.Konopka, S. Nijman. "GeneticThesaurus: Comparison of matched samples with thesaurus annotation" (under review)

Source code is developed by Tomasz Konopka.

Source code licence

Copyright 2013-2015 Tomasz Konopka

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

geneticthesaurus's Issues

Definition of the output BAF file columns

Dear @tkonopka ,

I'm trying to apply GeneticThesaurus to our WGS data.
Where could I look to know the definition of the output BAF files columns, especially sample.thesaurus.BAF, sample.naive.cov, and sample.thesaurus.cov?
My understanding is that sample.thesaurus.BAF is a BAF estimate when the alternate sites are considered and that the frequency ranges from 0 to 1.
However, it seems that some variants in my output BAF files have sample.thesaurus.BAF of >1, which I did not expect. Is my understanding incorrect?