### Variant Calling This APP developed for somatic short variant discovery (SNVs + Indels). ***Supported callers*** * TNhaplotyper2 * TNscope * VarScan * TNhaplotyper (This caller is only available in `v0.1.0` as it is too outdated) Variant caller can be selected by setting `ture/false` in the submitted sample.csv. ***Accepted data*** * TN matched WES * TN matched WGS The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs). ### New Releases * The TNhaplotyper, also named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2. * The `corealigner` step has been removed. ### Getting Started We recommend using choppy system and Aliyun OSS service. The command will look like this: ```Shell # Activate the choppy environment open-choppy-env # Install the APP choppy install YaqingLiu/variant-calling-latest [-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 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 * bed file * the caller you want to use * whether PoN needs to be set