Modes
In principle, the mgatk CLI will produce the same final output files for each of the major processing modes specified. However, depending on the source and format of your input data and the availability of computational resources, one should select which mode is best for them.
This mode functions as a drop-in for the examples shown above. Simply switch out bcall, call, or tenx with call and run your command with all appropriate flags. The mgatk main function will then attempt an execution and raise any problems (e.g. incorrect file paths, errant reference genome specification, or missing dependencies) prospectively. This is useful to make sure that you don't waste minutes or hours of your life only to realize that the genotyping command failed at the last step.
This is a simple mode that shows what built-in contigs are available:
Sun Aug 09 21:01:09 PDT 2020: mgatk v0.5.7
Sun Aug 09 21:01:09 PDT 2020: List of built-in genomes supported in mgatk:
Sun Aug 09 21:01:09 PDT 2020: ['GRCh37', 'GRCh38', 'GRCm38', 'GRCz10', 'NC_012920', 'hg19', 'hg19_chrM', 'hg38', 'mm10', 'mm9', 'rCRS']
Sun Aug 09 21:01:09 PDT 2020: Specify one of these genomes or provide your own .fasta file with the --mito-genome flag
See this part of the documentation if you don't see the reference genome of interest.
If you have a reference genome that you anticipate will be widely used but is currently absent, consider submitted a pull request with the .fasta file added to the fasta annotation package folder.
