2. Latest release notes and usage changes¶
2.1. Updates on this release¶
| Type | Description |
|---|---|
| Feature | Improved speed of BWA alignment. |
| Feature | Changed default CRAM output version to 3.0 |
| Feature | Reduced memory usage when outputting CRAM files. |
| Feature | Added error checking in tnhapfilter. |
| Feature | Improved accuracy of DNAscope model. |
| Feature | Removed Realigner stages from the example files |
| Feature | Added option in Haplotyer and GVCFtyper to use additional genotyping models. |
| Bug-fix | Solved issue in TNhaplotyer2 that could cause a run to run variation in the annotation calculation in 1 out of 100 runs. |
| Bug-fix | Solved issue in BWA that could cause an error when using an extremely large bwt_max_mem option. |
| Bug-fix | Solved issue that could cause an error when reading a CRAM file generated by cramtools. |
| Bug-fix | Improved error reporting. |
2.2. Usage changes from previous release¶
This released introduced the following changes in interface and usage:
- Added
--genotype_modeloption in Genotyper, Haplotyer and GVCFtyper algorithm to support new multinomial genotyping model.