VCF Toolz

Tools for working with Variant Call Format files.

VCF Toolz was developed by the United States Food and Drug Administration, Center for Food Safety and Applied Nutrition.

• Free software
• Documentation: https://vcftoolz.readthedocs.io
• Source Code: https://github.com/CFSAN-Biostatistics/vcftoolz
• PyPI Distribution: https://pypi.python.org/pypi/vcftoolz

Features

• Compares the snps in two or more VCF files.
• Lists the snps that are unique to each VCF file with full genotype information per snp.
• Lists the snps that are missing from each VCF file if present in at least two other VCF files.
• Generates Venn diagrams of positions and snps in the VCF files.
• Reports precision, recall, and F1 score when the truth is known.
• Reports the effectiveness of filtered variants when the truth is known.
• Reformat the VCF file in a tall-narrow format for easy viewing and diffs.
• Count samples, positions, calls, snps, indels, other variants, missing calls, and filter reasons.
• Plot calls along the length of the genome and show the location of filtered calls.

Citing VCF Toolz

To cite VCF Toolz, please reference the VCF Toolz paper:

https://doi.org/10.21105/joss.01144

License

See the LICENSE file included in the VCF Toolz distribution.