vcftoolz 1.2.3

Tools for working with Variant Call Format files.

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.

History

1.2.3 (2023-06-02)

• Fixed imports in our fork of pyvenn

1.2.2 (2023-06-01)

• Fixed broken Pyvenn dependency

1.2.1 (2023-05-09)

• Update PyVCF to PyVCF3

1.2.0 (2019-04-04)

• Fix defect in narrow command wrongly printing ALT=. when GT=.

• Add the count command to count samples, positions, calls, snps, indels, other variants, filtered calls, missing calls, and filter reasons.

• Add the plot command to plot calls along the length of the genome and show the location of filtered calls.

• Change the text of the compare report to refer to “Calls”, not “Sample snps”.

• Drop support for Python 3.4, which is not supported by matplotlib.

• Add support for Python 3.7.

1.1.1 (2019-03-26)

• Replace None with ‘.’ when printing call data.

• Support VCF files with multiple alternate alleles per position.

1.1.0 (2019-02-06)

• Support reading gzip compressed vcf files.

1.0.0 (2018-11-20)

• First public release.