Up: Component summary
Up: Component summary
Component
Annovar
The component annotates genetic variants using ANNOVAR (table_annovar). The annotations are specified via the parameters "protocol" and "operation", using annotation database files located in the "annovardb" directory. The variants input can be either VCF or CSV file and the output will have the same format as the input. When using CSV input, make sure you
have the right format that is the first five columns are chr,start,end,ref,alt (name doesn't matter). To make sure your variants are in the correct format (especially for indels), you may want to use the convert2annovar.pl
for creating the csv input. Otherwise, VCF annotation can be done directly. Check ANNOVAR documentation for more information. The component is developed on ANNOVAR version 20160201 so make sure you have
as recent version.
| Version | 1.0 |
|---|---|
| Bundle | sequencing |
| Categories | Annotation VariationAnalysis |
| Authors | Amjad Alkodsi (Amjad.Alkodsi@Helsinki.FI) |
| Issue tracker | View/Report issues |
| Requires | Annovar |
| Source files | component.xml Annovar.sh |
| Usage | Example with default values |
Inputs| Name | Type | Mandatory | Description |
|---|---|---|---|
| csvIn | CSV | Optional | Variants in CSV format. The first five columns should be chr,start,end,ref,alt |
| vcfIn | VCF | Optional | Variants in VCF format. |
Outputs| Name | Type | Description |
|---|---|---|
| csvOut | CSV | Annotated variants in CSV format. Empty if VCF input was used |
| vcfOut | VCF | Annotated variants in VCF format. Empty if CSV input was used. |
| analysis | BinaryFolder | Folder having intermediate results. |
Parameters| Name | Type | Default | Description |
|---|---|---|---|
| annovarPath | string | "" | Path where table_annovar can be found. If empty, ANNOVAR_HOME will be used |
| annovardb | string | "" | Path to annovardb folder. If empty ANNOVARDB_HOME will be used |
| argument | string | "" | values to be passed to the annovar argument parameter. If empty, argument parameter will not be used |
| buildver | string | "hg19" | Genome build version like hg19, hg18, hg38. Check Annovar documentation for accepted versions |
| inputType | string | "vcf" | Input type which can be csv or vcf |
| operation | string | (no default) | comma-sepparated values of operation types e.g. "g,r,f". The number of values should match the number of protocols |
| options | string | "" | Extra options to be passed to table_annovar |
| protocol | string | (no default) | Comma-separated values for databases to use e.g. "refGene,cytoBand,cadd". Check annovar documentation for available databases. Databases files should be downloaded in your annovardb folder |
| threads | int | 1 | Number of threads |
Test cases| Test case | Parameters▼ | IN csvIn |
IN vcfIn |
OUT csvOut |
OUT vcfOut |
OUT analysis |
|---|---|---|---|---|---|---|
| case1 | properties | csvIn | (missing) | (missing) | (missing) | (missing) |
|
protocol=refGene, |
||||||
| case2 | properties | (missing) | vcfIn | (missing) | (missing) | (missing) |
|
protocol=refGene, |
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