msk-access / genotype_variants

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 v1.2.5 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.

genotype_variants's Issues

create_all_maf_dataframe.py

• genotype_variants version: current
• Python version: 3.7.4 installed via Miniconda
• Operating System: CentOS-7 running on Juno

Description

Running genotype_variants small_variants all using the command line below. The underlying file create_all_maf_dataframe.py contains errors which prevent python from combining the maf files produced from the previous steps

What I Did

1/ Line #111
df_ds refers to the combined duplex simplex data frame whilst df_s which receives the value of the operation is a subtraction of df_ds from another field in df_s. df_ds does not contain a column with name t_total_count_forward_standard since only df_s was renamed at Line #73-81

2/ Line #133 and #147, df_d is undefined