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Tools for working with Variant Call Format files.

Project description

https://img.shields.io/pypi/v/vcftoolz.svg http://joss.theoj.org/papers/10.21105/joss.01144/status.svg

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.
  • 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

1.2.0 (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.

Project details


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