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VCF to VariantDB (version 0.1.3)

VCF file:

Select variant file to import

VCF Source Application:

Supported formats are VCF from UnifiedGenotyper, HaplotypeCaller, Mutect and VarScan

Store VCF and BAM Files::

This option allows you to send the BAM and VCF files to our storage server for dynamic loading into IGV. If you store them there, please delete them here.

Provide a Sample Name ::

If no name is specified, a new sample will be created, and you will be notified of the name

Sample Name.:

Sample Gender: :

This can be set from the database frontend as well.

VariantDB-Server: :

Specify the VariantDB server you wish to send the data to. You MUST have a valid account on the target server, identical to your account here.

What it does

This tools sends VCF files with results from the GATK unified genotyper, HaploType Caller, Mutect or samtools VarScan to a VariantDB server. From there, variants can be compared between samples, filtered on various annotations etc. To add servers, specify them in the tool configuration XML file.

Input file

VCF file from the GATK Unified Genotyper.

Outputs

Text file with some results from the vcf-parser.