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| **Supported variant callers and annotation tools** | **Supported variant callers and annotation tools** | ||||
| * Variant calling: | |||||
| - `haplotyper` (germline) | |||||
| - `tnseq`, `tnscope`, `varscan` (somatic) | |||||
| * Variant calling: `haplotyper` (germline); `tnseq`, `tnscope`, `varscan` (somatic). | |||||
| * 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. | ||||
| * the caller you want to use. | * the caller you want to use. | ||||
| * PoN VCFs for TNseq and TNscope is supported, but are need to be generated in advance. | * PoN VCFs for TNseq and TNscope is supported, but are need to be generated in advance. | ||||
| * interval padding is default 0, and you can change it. | * interval padding is default 0, and you can change it. | ||||
| * the annotation tool is ANNOVAR or VEP. | |||||
| * usually only one annotation tool is sufficient. |
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