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Tools for working with Variant Call Format files.

Project description

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.


  • 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.

Citing VCF Toolz

To cite VCF Toolz, please reference the VCF Toolz GitHub repository:


See the LICENSE file included in the VCF Toolz distribution.


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.

Project details

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vcftoolz-1.1.1.tar.gz (31.2 kB view hashes)

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