### 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callers*** * TNhaplotyper2 * TNscope * VarScan * TNhaplotyper (This caller is only available in `v0.1.0` as it is too outdated) Variant caller can be selected by setting `ture/false` in the submitted sample.csv.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 * WGS The datatype is judged by whether the bed file is set (i.e. the `regions` in inputs). ### New version * The TNhaplotyper, also named as TNseq in `v0.1.0`, has beed substituted by TNhaplotyper2. * The `corealigner` step has been removed. ### How to run this APP We recommend using choppy system and Aliyun OSS service. The command will look like this: ``` open-choppy-env choppy install YaqingLiu/variant-calling-latest choppy samples YaqingLiu/variant-calling-latest --no-default # sample_id,normal_fastq_1,normal_fastq_2,tumor_fastq_1,tumor_fastq_2 choppy batch YaqingLiu/variant-calling-latest samples.csv -p Project -l 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. **Please carefully check** * the reference genome * bed file * the caller you want to use * whether PoN needs to be set