2. Latest release notes and usage changes¶
2.1. Updates on this release¶
| Type | Description |
|---|---|
| Feature | Improved speed of TNscope. |
| Feature | Added option --trim_soft_clip to TNscope, TNhaplotyper and TNHhaplotyper2. |
| Feature | Added capability for output BAM from --bam_output option to keep the input BAM RG information. |
| Feature | Added option --disable_detector to TNscope to control the type of variants called. |
| Feature | Added support in TNscope SV calling to more accurately represent large INS. |
| Feature | Added mode to util fqidx to extract a fraction of the reads. |
| Feature | Added support in GVCFtyper merge mode to allow input files hosted in an object storage location. |
| Feature | Added support for using multiple --interval options. |
| Bug-fix | Solved issue in TNscope that could call a false positive in a site that has a germline call and is neighboring another SNV. |
| Bug-fix | Improved error reporting. |
| Bug-fix | Solved issue in sentieon script that could prevent using a demo license on a shell that is not BASH. |
| Bug-fix | Solved issue that would prevent BED files containing an interval with identical start and end. |
| Bug-fix | Solved issue in DNAModelApply that would cause an error when the input VCF file is empty. |
| Bug-fix | Solved issue in plot that could cause it to run longer than necessary. |
| Bug-fix | Solved issue in DNAModelApply that would cause an error when over-scheduling. |
| Bug-fix | Solved issue in util sort that could cause an assertion error when over-scheduling. |
| Bug-fix | Solved issue in plot that would generate BQSR PDF plots without AA and AAA context covariate. |
2.2. Usage changes from previous release¶
This released introduced the following changes in interface and usage:
- Added TNscope option --disable_detector to control the type of variants called.
- Added support for using multiple --interval options.