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README.md
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| ### Variant Calling | ### Variant Calling | ||||
| 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 WES for somatic variant calling | ||||
| * TN matched WGS for somatic variant calling | * TN matched WGS for somatic variant calling | ||||
| * Normal-only WES for germline variant calling | * Normal-only WES 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 Callers** | |||||
| **Supported Callers** | |||||
| * The fields corresponding to these callers include `haplotyper`, `tnseq`, `tnscope`, `varscan`. | * The fields corresponding to these callers include `haplotyper`, `tnseq`, `tnscope`, `varscan`. | ||||
| * All callers are <u>**not activated by default**</u>, which means the default setting is `false`. | * All callers are <u>**not activated by default**</u>, which means the default setting is `false`. | ||||
| * TNscope | * TNscope | ||||
| * VarScan | * VarScan | ||||
| --- | |||||
| >**Annotation Tools** | |||||
| **Annotation Tools** | |||||
| * The fields corresponding to two tools include `annovar`, `vep`. | * The fields corresponding to two tools include `annovar`, `vep`. | ||||
| * All tools are <u>**not activated by default**</u>, which means the default setting is `false`. | * All 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. | * You need to manually set the caller to `true` in the submitted sample.csv. |
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