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| This APP developed for germline and somatic short variant discovery (SNVs + Indels). | This APP developed for germline and somatic short variant discovery (SNVs + Indels). | ||||
| **Accepted data** | **Accepted data** | ||||
| * TN matched WES for somatic variant calling | |||||
| * TN matched WGS for somatic variant calling | |||||
| * Normal-only WES for germline variant calling | |||||
| * Normal-only WGS for germline variant calling | |||||
| * TN matched or tumor-only WES/WGS for somatic variant calling | |||||
| * Normal-only WES/WGS for germline variant calling | |||||
| The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs). | The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs). | ||||
| **Supported variant callers and annotation tools** | **Supported variant callers and annotation tools** | ||||
| * Variant calling: `haplotyper` (germline); `tnseq`, `tnscope`, `varscan` (somatic). | |||||
| * Variant calling: `haplotyper`, `pindel` (germline); `tnseq`, `tnscope`, `varscan` (somatic; `varscan` don't support the variant calling of tumor-only data). | |||||
| * Annotation: `annovar`, `vep`. | * Annotation: `annovar`, `vep`. | ||||
| * The above tools are <u>**not activated by default**</u>, which means the default setting is `false`. You need to manually set the caller to `true` in the submitted sample.csv. | * The above tools are <u>**not activated by default**</u>, which means the default setting is `false`. You need to manually set the caller to `true` in the submitted sample.csv. | ||||
| ### New Releases | ### New Releases |
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