Introduction

wANNOVAR is a web server that provides easy and intuitive web-based access to the most popular functionalities of the ANNOVAR software. Users can upload a VCF file and obtain annotated results as tab-delimited or comma-deleted files; in addition, simple variants reduction can be performed to prioritize deleterious variants from the input files. Currently, wANNOVAR supports only human genome annotation.

Below we describe the input fields and output format in wANNOVAR.


Basic Information

What should be noticed is, as the program usually takes more than 5 minutes, thus a valid email is required here, in case you forgot the link. If the program runs very well, we will send you an email later.

Identifier is just the name of your program. You can give a name as to your own preference, like 'Jim's awesome run', 'My first run', '1122233', so on. When you click the 'Monitor Progress' button, you can recognize your program by your specific identifier.

This is the place where you should submit your variant calls, either by a file or through paste.

Five different types of formats could be accepted here, separately, vcf, tsv, annovar, gff3 and masterVar. The details of these formats could be seen through the Zoom In icon in the Parameter Setting section.


Phenotype/Disease Specific Prioritization

Phenolyzer stands for Phenotype Based Gene Analyzer, a new software developed by us, which can prioritize genes based on specific diseases or phenotypes. Call Phenolyzer is a pipeline connecting wANNOVAR with Phenolyzer, discovering genes directly from wANNOVAR output. It is extremely helpful if the user provides some short disease/phenotype terms together with the variant file, then robust ontology searching and machine learning method is used to discover the candidate genes.

To see more Phenolyzer examples, please click this link

To see the FAQ of Phenolyzer, please click this link

Enter Phenotypes or Diseases here. Please enter some terms here if you already have an idea about which disease/phenotype you are interested in or already observed. Several kinds of terms are accepted here, including:

  1. disease names: like alzheimer, parkinson, chron, and so on;
  2. phenotype names: like fatigure, Blood pressure. Any HPO (Human Phenotype Ontology) term is also accepted.
  3. OMIM IDs: like 114480 for'breast cancer'.

Please use Enter or ';' as separators, some other non-word characters are also acepted like '|'.

Please try to use short terms instead a very long term. As the first step of Phenolyzer is to do word match between your word and the names in our database. Thus super long names might not have any results.

For example, 'X-linked intellectual deficiency' is better to be separated into 'X-linked' and 'intellectual deficiency'.

If any Phenotype/Disease terms are entered, there will be an addtional section in the result, named 'Phenotype/disease Prioritization Result'.

The first row 'Input Gene List' is the gene list extracted from the ANNOVAR output variant calling list.

Tip: After your first run of wANNOVAR, you can run Phenotype/Disease specific prioritization with some other terms without the need to run wANNOVAR, which is more time and computation efficient as Phenolyzer could finish in one minute and wANNOVAR usuually takes more than 5 minutes. What you need to do is just take the Input Gene List here, go to Phenolyzer website and submit it and your new phenotypes there!

In the result page, 'Result Gene List' is the output from Phenolyzer, with the information of ranks, gene names, NCBI IDs, and scores. 'Show' will lead you to the Phenolyzer's network visualization. You could do interactive research there, like finding all the genes and diseases interacting with one gene by double click the gene. You can also see the details about how one gene is discovered through the prioritization algorithm.


Parameter Setting

This part is mainly for advanced settings of wANNOVAR. You can change the genome build, input format, gene definition, and disease filter here. The details of them could be found by clicking the 'Zoom in' button following each input element.

Advanced Notes: If you use the custom filtering option, please at least choose a filter step in the section below, or use a control file.

- Reference Genome

- Input Format

- Gene Definition

- Disease Model

- Custom Filtering


Result Description

The basic section in the result page. In all cases you should see this part

The variant filtration/reduction part and the phenotype based prioritization part

Table below lists the some columns of variants annotation from wANNOVAR. For other details, please see ANNOVAR website: region based annotation and filter based annotation.

Column Name Explanation
Func Variant function (exonic, intronic, intergenic, UTR, etc)
Gene Gene Name. By default, RefSeq gene definition is used, but users can choose from other gene definition systems.
ExonicFunc Exonic variant function (non-synonymous, synonymous, etc)
AAChange Amino acid changes
Conserved Region-level phastCons LOD scores