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This article mainly introduces what kind of software oncotator is, has a certain reference value, interested friends can refer to, I hope you can learn a lot after reading this article, the following let the editor take you to understand it.

At present, there are three kinds of popular mutation annotation software.

ANNOVAR

SnpEff

Variant Effect Predictor (VEP)

These three softwares have a wide range of applications and can annotate any genomic variation, whether it's germline or somatic variants. At the same time, the problem is that for tumor genome research, the annotation results are lack of tumor-specific annotation content, and the annotation results are in VCF format, which needs to be further converted to MAF format in order to carry out downstream analysis of tumor research, which is not convenient.

To solve this problem, Broad Institute scientists have developed an annotation software called oncotator, which is specially designed for tumor genome research. The annotation results can be directly output to MAF format. The official website is as follows.

Https://software.broadinstitute.org/cancer/cga/oncotator

The software integrates annotation information from 14 different sources and is divided into the following four categories

Genomic Annotations

Protein Annotations

Cancer Variant Annotations

Non-Cancer Variant Annotations

The databases corresponding to different categories are shown as follows

The source code of the software is saved on github at the following URL

Https://github.com/broadinstitute/oncotator/releases

At the same time, the software relies on an integrated database, which can be downloaded as follows

Wget-r "ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/oncotator/"

The size of the database is 17G, and the software is developed by python. The installation process is relatively simple, and the basic usage is as follows.

Oncotator\

-v\

-- db-dir / oncotator_v1_ds_Jan262015\

-- input_format=VCF\

-- output_format=TCGAMAF\

Input.vcf\

Output.maf\

Hg19

The db-dir parameter specifies the path to the downloaded data database, and the last three parameters correspond to the input file, output file and genome version. The software only supports the hg19 version.

For the convenience of researchers with no programming experience, web services are also provided at the following website

Http://portals.broadinstitute.org/oncotator/

Upload the abrupt data in tsv format, as shown below

The results are shown as follows

Through this software, we can get the comment file in MAF format, which is more convenient for downstream data analysis.

Thank you for reading this article carefully. I hope the article "what kind of software oncotator is" shared by the editor will be helpful to everyone. At the same time, I also hope you will support us and pay attention to the industry information channel. More related knowledge is waiting for you to learn!

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