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 v1.2.5 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.
2 maintainers
Metadata
2 maintainers
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