genotype_variants GitHub Workflow Status Documentation Status

Project to genotype SNV, INDELS and SV.


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 ( section of the documentation for more information

Requires GetBaseCountMultiSample v1.2.5 and above

To Do

  • Tagging genotyped files for thresholds
  • Genotyping normal buffy coats
  • Genotype structural variants calls


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