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BAM

Node extension for KNIME Workbench version 1.0.24 by Pierre Lindenbaum

Displays a local BAM file using the Picard API. Not, this node still needs to be refreshed after each KNIME session. The first table contains the VCF results. The second table contains the sample name and the path to a BAM file.

References

Knime4Bio. Author: Pierre Lindenbaum PhD, INSERM UMR 915, Institut du thorax, Nantes. Reference: manuscript in preparation. Please, report any problem here.
This nodes uses the Picard Library to read the BAMs.

Options

CHROM: The VCF CHROM column
POS: The VCF POS column. The genomic position (1-based)
sample1: The Sample Column in the first table
uri: The full path to a BAM file in 2nd table
sample2: The Sample Column in the 2nd table

Input Ports

: A VCF-like table (CHROM/POS/SAMPLE)
: A table with two columns: Sample and full path to BAM file

Views

view bam: View Bam

Installation

To use this node in KNIME, install Node extension for KNIME Workbench from the following update site:

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