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
- 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.
To cite VCF Toolz, please reference the VCF Toolz paper:
https://doi.org/10.21105/joss.01144
See the LICENSE file included in the VCF Toolz distribution.