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Bcftools

IBIS Helmholtz-Node extension for KNIME Workbench version 1.8.1.201707071203 by IBIS KNIME Team

BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF.
Source: https://samtools.github.io/bcftools/bcftools.html

Options

Method Selection
Select a method for execution. Currently the node includes:
  • index: Creates an index for bgzip compressed VCF/BCF files for random access.
  • concat: Concatenate or combine VCF/BCF files.
  • reheader: Modify header of VCF/BCF files, change sample names.
  • stats: Parses VCF or BCF and produces text file stats which is suitable for machine processing and can be plotted using plot-vcfstats.
Sample Name File
File with new sample names, one name per line, in the same order as they appear in the VCF file. Alternatively, only samples which need to be renamed can be listed as "old_name new_name\n" pairs separated by whitespaces, each on separate line.
Further Parameters
Further parameters can be added to the execution command if necessary.

Concat

Overlap
First coordinate of the next file can precede last record of the current file.
Output format
Select output format.

Preference page

HTE
Set threshold for repeated execution. Only used if HTE is enabled in the preference page.
Path to bcftools
Select bcftools executable in the Samtools/Bcftools folder. This option is disabled if the path is set using the preference page.

Input Ports

Icon
Cell 0..n: Path to Input file(s)

Output Ports

Icon
Cell 0: Path to Output file

Views

STDOUT / STDERR
STDOUT / STDERR

Installation

To use this node in KNIME, install KNIME4NGS from the following update site:

KNIME 4.3

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Developers

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