vcftoolz 1.2.3

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.

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.