GenotypeGVCFs

GenotypeGVCFs merges gVCF records that were produced by the HaplotypeCaller, or result from combining such gVCF files using CombineGVCFs. This tool performs the multi-sample joint aggregation step and merges the records together in a sophisticated manner: at each position of the input gVCFs, this tool will combine all spanning records, produce correct genotype likelihoods, re-genotype the newly merged record, and then re-annotate it.
For further information, see GATK documentation of GenotypeGVCFs.

Options

Number of threads

Set the number of threads to be used. Increasing the number of threads speeds up the node, but also increases the memory required for the calculations.

Folder for output files

Set the path to the folder where the output files should be stored.

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 GenotypeGVCFs.

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