NGSCheckMate_parallel/README.md

### NGSCheckMate
A C program, ngscheckmate_fastq, can be directly called to generate a VAF file from one FASTQ file (single-end sequencing) or two FASTQ files(paired-end sequencing). 

Then, another script, vaf_ncm.py is used to read a set of VAF files to complete the downstream analysis. When you need to analyze many FASTQ files, the first VAF file generation using ngscheckmate_fastq can be parallelized.

**If you want to analyze the correlation of samples over multiple runs, I suggest you to save the historical `vaf` files and download the NGSCheckMate from https://github.com/parklab/NGSCheckMate and then run vaf_ncm.py locally.**
### 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/NGSCheckMate_parallel-latest [-f]

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

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

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

#### samples.json
``` json
{
  "sample_id": "test", 
  "fastq1": ["fq1_1", "fq1_2", ..., "fq1_n"],
  "fastq2": ["fq2_1", "fq2_2", ..., "fq2_n"],
  "output_id": ["out_id1", "out_id2", ..., "out_idn"]
}
```

#### other parameters
subsampling_rate: The default subsampling rate is 1. The speed is not very slow.
-f in vaf_ncm.wdl: Use strict VAF correlation cutoffs. Recommended when your data may include related individuals (parents-child, siblings).