Joint variant calling with GATK4 HaplotypeCaller, Google DeepVariant 1.0.0 and Strelka2, coordinated via Snakemake.
We have written a bcftools plugin exchangeGT for the users to swap one of the GT fields, such as DV_GT, HC_GT and strelka2_GT, dv_priority_GT or concensus_GT as the main GT, it can be find in the bcftools_plugin directory in this repository.
To use it, please checkout the bcftools GitHub repository, copy exchangeGT.c to its plugins directory and follow its installation directions here to install it.
You can get a list of options by:
bcftools +exchangeGT