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Annovar

The component annotates variants using Annovar (table_annovar). The 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 Analysis
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-sepparated 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,
operation=g,
inputType=csv,
annovardb=/opt/share/annovar_20160201/annovar/humandb,
annovarPath=/opt/share/annovar_20160201/annovar

case2 properties (missing) vcfIn (missing) (missing) (missing)

protocol=refGene,
operation=g,
annovardb=/opt/share/annovar_20160201/annovar/humandb,
annovarPath=/opt/share/annovar_20160201/annovar


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