GATKSelectVariants

This node is based on the SelectVariants tool of GATK. It can be used for selecting subsets of variants from a VCF containing many samples and/or variants.
For further information, see GATK documentation of SelectVariants.

Options

Select Variant Type

Select the variant type (SNP or indel) which should be in the resulting subset file.

GATK

GATK Memory

Set the maximum Java heap size (in GB).

Path to BED file

You can check this option to perform the analysis in certain genomic regions. You have to specify the intervals in a text file in BED format and select the file in the file browser.

Further options

Set additional command line flags for the GATKSelectVariants.

Preference page

HTE

Set a threshold for repeated execution. Only used if HTE is enabled in the preference page.

Path to reference sequence

Set the path to the reference reference sequence. This will be done automatically if the path is already defined in the preference page.

Path to GATK jar file

Set the path to GenomeAnalysisTK.jar. This will be done automatically if the path is already defined in the preference page.

Views

STDOUT / STDERR

The node offers a direct view of its standard out and the standard error of the tool.

Workflows

• No workflows found

Links

• No links available

Developers