genotype-variants 0.3.5

Project to genotype SNV, INDEL and SV.

genotype_variants

Project to genotype SNV, INDELS and SV.

• Free software: Apache Software License 2.0

• Documentation: https://genotype-variants.readthedocs.io.

Features

Currently this module only supports genotyping and merging small variants (SNV and INDELS).

For this we have the following command line submodule called small_variants.

Which have the following sub-commands:

• generate: To run GetBaseCountMultiSample version 1.2.5 on given BAM files

• merge: To merge MAF format files w.r.t counts generated from the generate command.

• all: This will run both of the sub-commands above generate and merge togather.

• multiple-samples: This will run sub-commands all for multiple samples in the provided metadata file

Please read the USAGE (https://genotype-variants.readthedocs.io/en/latest/usage.html) section of the documentation for more information

Requires GetBaseCountMultiSample v1.2.4 and above

To Do

• Tagging genotyped files for thresholds

• Genotyping normal buffy coats

• Genotype structural variants calls

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

History

0.3.0 (2020-04-10)

• Release with merge for standard BAM maf and Input MAF. Converted multiple-patient to multiple-sample

0.2.1 (2020-04-09)

• Release bug fixes, where simplex numbers are listed as duplex and vice versa, during running all command.

0.2.0 (2020-04-08)

• Release with multiple-patient command.

0.1.0 (2020-01-30)

• First release on PyPI.