Bcftools

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.

Views

STDOUT / STDERR

STDOUT / STDERR

Workflows

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Links

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Developers