variant-calling/README.md

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

**Accepted Data**
* TN matched WES for somatic variant calling
* TN matched WGS for somatic variant calling
* Normal-only WES for germline variant calling
* Normal-only WGS for germline variant calling

The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs).

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**Supported Callers**

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

<u>***Germline***</u>
* Haplotyper

<u>***Somatic***</u>
* TNseq (TNhaplotyper2)
* TNscope
* VarScan

---

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

### New Releases
* TNhaplotyper, named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2.
* The `corealigner` step has been removed.
* The `vcf2maf` step has been removed. Thus, the final output is the annotated `VCF`.
* Some parameters' details have been changed, such as the `interval_list` has turned into `interval`.

### Getting Started

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

```
# Activate the choppy environment
$ open-choppy-env

# Install the APP
$ choppy install YaqingLiu/variant-calling [-f]

# List the parameters
$ choppy samples YaqingLiu/variant-calling-latest [--no-default]

# Submit you task with the `samples.csv file` and `project name`
$ choppy batch YaqingLiu/variant-calling-latest samples.csv -p Project [-l project:Label]

# Query the status of all tasks in the project
$ choppy query -L project:Label | grep "status"
```

**Please note:** The `defaults` can be forcibly replaced by the settings in `samples.csv`. Therefore, there is no need to contact me over this issue.

The parameters that must need contains: sample_id,normal_fastq_1,normal_fastq_2,tumor_fastq_1,tumor_fastq_2


**Please carefully check**
* the reference genome you want to use is hg38 or hg19.
* bed file.
* the caller you want to use.
* 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.
* the annotation tool is ANNOVAR or VEP.