17eb7b49fe
There is now a command-line option to set the model to use in the HC. Incorporated Ryan's current (unmerged) branch in for most of these changes. Because small changes to the math can have drastic effects, I decided not to let users tweak the calculations themselves. Instead they can select either NONE, CONSERVATIVE (the default), or AGGRESSIVE. Note that any base insertion/deletion qualities from BQSR are still used. Also, note that the repeat unit x repeat length approach gave very poor results against the KB, so it is not included as an option here. |
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| .. | ||
| annotator | ||
| beagle | ||
| bqsr | ||
| compression/reducereads | ||
| diagnostics | ||
| diffengine | ||
| fasta | ||
| filters | ||
| genotyper | ||
| haplotypecaller | ||
| indels | ||
| phasing | ||
| validation | ||
| varianteval | ||
| variantrecalibration | ||
| variantutils | ||