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Tools for working with Variant Call Format files.

Project description

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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.

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.

Citing VCF Toolz

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

https://github.com/CFSAN-Biostatistics/vcftoolz

License

See the LICENSE file included in the VCF Toolz distribution.

History

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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Source Distribution

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

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