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### Variant calling
This APP developed for somatic short variant discovery (SNVs + Indels). This APP developed for somatic short variant discovery (SNVs + Indels).



***Supported callers*** ***Supported callers***
* TNhaplotyper2 * TNhaplotyper2
* TNscope * TNscope
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).




#### New version
### New version
* The TNhaplotyper, also named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2. * The TNhaplotyper, also named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2.
* The `corealigner` step has been removed. * The `corealigner` step has been removed.


#### How to run this APP
### How to run this APP


We recommend using choppy system and Aliyun OSS service. The command will look like this: We recommend using choppy system and Aliyun OSS service. The command will look like this:



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