This is a wrapper node for Pindel (designed for version 0.2.4) and the Pindel2VCF converter.
Pindel is a tool for identifying structural variants in paired-end Illumina reads.
It finds large deletions, medium-sized insertions, inversions and tandem duplications.
Currently, this node only focuses on the deletions and short insertions called by Pindel and it is compatible with mappings produced by BWA or MOSAIK only.
As Pindel has its own output format, this node includes also the Pindel2VCF script.
It converts the files produced by Pindel to VCF format (Format explained at http://www.1000genomes.org/wiki/analysis/variant-call-format/VCF-variant-call-format-version-42 ).
Further information about Pindel and installation instructions are available at http://gmt.genome.wustl.edu/packages/pindel/
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To use this node in KNIME, install the extension KNIME4NGS from the below update site following our NodePit Product and Node Installation Guide:
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