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updated readme
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zhengzhenxian committed Sep 18, 2023
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### PacBio Revio SNV performance

- HCC1395/HCC1395BL tumor/normal of PacBio Revio data, using SMRTbell prep kit 3.0
- Truth:High confidence (HighConf) and medium confidence (MedConf) SNV from the SEQC2 HCC1395/BL truths ([Fang et al., 2021](https://www.nature.com/articles/s41587-021-00993-6)), the TVAF (tumor variant allele frequency) of which is ≥0.05 in the above dataset

#### The performance of ClairS at multiple VAF ranges and multiple tumor coverages with the normal coverage fixed at 25x

![](./images/hifi_vaf_1_result.png)

#### The performance of ClairS at multiple VAF ranges and multiple normal coverages with the tumor coverage fixed at 50x

![](./images/hifi_vaf_2_result.png)



### Illumina SNV performance

- HCC1395/HCC1395BL tumor/normal of of Illumina NovaSeq 6000 and HiSeq 4000 data
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## Latest Updates
*v0.1.6 (Sep 18)* : 1. Fixed an output bug that caused no VCF output if no Indel candidate was found (contributor @[Khi Pin](https://github.com/proteinosome)). 2. Fixed showing incorrect reference allele depth at a deletion region. 3. Added PacBio HiFi [quick demo](docs/pacbio_hifi_quick_demo.md).

*v0.1.5 (Aug 2)* : 1. Updated SNV calling using ONT Dorado 4kHz data with a new model trained using multiple-sample pairs (HG003/4); 2. Updated SNV calling using ONT Dorado 5kHz data with a new model trained using multiple-sample pairs (HG001/HG002, HG003/4); 3. Support somatic indel calling using ONT Dorado 4kHz data. 4. Support somatic indel calling using ONT Dorado 5kHz data.

*v0.1.4 (Jul 15)* : 1. Added reference depth in AD tag. 2. Added HiFi Sequel II Indel model.
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