[[release v2.0.0](https://github.com/ShujiaHuang/ilus/releases/tag/v2.0.0)] - 2023-12-05
What's new
- **Enable raw fastq data filtering by using [SOAPnuke](https://github.com/BGI-flexlab/SOAPnuke)**.
- **Enable to create pipeline for WES or other kinds of capture sequencing data**.
- **Add [Sentieon](http://sentieon.com/about/) mudules. Enable to create WGS/capseq analysis pipeline by using Sentieon**
- **Rewrite the format of the configuration file**.
Update details
- Rewrite the format of configuration file, isolated the `resources` option from `gatk` section as a new section to facilitate shared use by `Sentieon` and `GATK`.
- Added `sentieon` module and constructed WGS/WES analysis workflows based on `sentieon`.
- Removed the `--max-gaussians` option from the `vqsr_options` in the configuration file and replaced it with separate settings for SNP (`vqsr_snp_max_gaussians`) and Indel (`vqsr_indel_max_gaussians`).
- Moved the calculation of alignment statistics and data contamination section out from `BQSR` section to `bwamem` section. Changed the suffix from `.recal.table` to `.BQSR.recal.table`.
- Added the `--dbsnp` parameter for `genotypeGVCFs` to annotate known sites.
- Added fastq data filtering module based on `SOAPnuke`.
- Encapsulated the `gatk` module as a GATK class.
- Added the `--interval` parameter for WGS as the variant-calling-interval.
- Added a parameter to the workflow to automatically remove unnecessary sub-vcfs for WGS/WES.
- Rewrote the `genotype-joint-calling` module, allowing the first column of the input parameter `gvcf.list` to contain arbitrary interval information, including `chromosome ID`, `chr:start-end`, or a `.bed` file.