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YaqingLiu 4 年前
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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).


***Supported callers***
**Supported callers**


All callers are **not activated by default**, which means the default setting is `false`.
* All callers are **not activated by default**, which means the default setting is `false`.
* You need to manually set the caller to `true` in the submitted sample.csv.
* The fields corresponding to these callers include `haplotyper`, `tnseq`, `tnscope`, `varscan`.


You need to manually set the caller to `true` in the submitted sample.csv.

The fields corresponding to these callers include `haplotyper`, `tnseq`, `tnscope`, `varscan`.

**Germline**
***Germline***
* Haplotyper * Haplotyper


**Somatic**
***Somatic***
* TNseq (TNhaplotyper2) * TNseq (TNhaplotyper2)
* TNscope * TNscope
* VarScan * VarScan
* TNhaplotyper (This caller is only available in `v0.1.0` as it is too outdated) * TNhaplotyper (This caller is only available in `v0.1.0` as it is too outdated)


***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

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