Project to genotype SNV, INDELS and SV.
- Free software: Apache Software License 2.0
- Documentation: https://genotype-variants.readthedocs.io.
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 v1.2.5 and above
- 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.