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@@ -13,9 +13,7 @@ The datatype is judged by whether the bed file is set (i.e. the `regions` in inp |
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**Supported variant callers and annotation tools** |
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* Variant calling: |
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- `haplotyper` (germline) |
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- `tnseq`, `tnscope`, `varscan` (somatic) |
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* Variant calling: `haplotyper` (germline); `tnseq`, `tnscope`, `varscan` (somatic). |
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* Annotation: `annovar`, `vep`. |
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* 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. |
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@@ -57,4 +55,4 @@ The parameters that must need contains: sample_id,normal_fastq_1,normal_fastq_2, |
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* the caller you want to use. |
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* PoN VCFs for TNseq and TNscope is supported, but are need to be generated in advance. |
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* interval padding is default 0, and you can change it. |
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* the annotation tool is ANNOVAR or VEP. |
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* usually only one annotation tool is sufficient. |