GATKHaplotypeCaller

This node is based on the HaplotypeCaller tool of GATK. It is capable of calling SNPs and indels simultaneously via local de-novo assembly of haplotypes in an active region. In the so-called GVCF mode used for scalable variant calling in DNA sequence data, this tool runs per-sample to genrate a intermediate genomic gVCF, which can then be used for joint genotyping of multiple samples.
For further information, see GATK documentation of the HaplotypeCaller.

Options

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 GATKHaplotypeCaller.

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

• KNIME4NGS_Test_VarCallingKnime4NGS

Links

• No links available

Developers