anvi-script-variability-to-vcf

Authors
Requires
Provides
Usage
Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

A script to convert SNV output obtained from anvi-gen-variability-profile to the standard VCF format.

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Authors

Srinidhi Varadharajan

Requires

variability-profile-txt

Provides

vcf

Usage

This script converts a variability-profile-txt into vcf (Variant Call Format).

It is very easy to run: just provide the input and output paths as so:

anvi-script-variability-to-vcf -i variability-profile-txt \ -o vcf

Note that to run this, you’ll need to have run anvi-gen-variability-profile with the default nucleotide engine.

Edit this file to update this information.

Command line interface

The following is the list of parameters and their descriptions in the latest version of anvi-script-variability-to-vcf.

The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).

Command line usage

anvi-script-variability-to-vcf [-h] [-i FILE_PATH] [-o FILE_PATH]

Parameters and their descriptions

options

-i, --input FILE_PATH: Filepath to the SNV table. This is the output from the anvi-gen-variability-profile program with the nucleotide engine (which is the default engine).
-o, --output-file FILE_PATH: File path to store results.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.