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sentieon

GATK best practice variant calling pipeline implements with license server for Sentieon

.
├── Jobs    
│   ├── run_Jobs.pl
│   ├── variant_calling.sh
│   ├── check_Jobs.sh
│   ├── _rc_function_.sh
│   ├── test_list.txt
│   ├── Outputs
│   └── logs
├── Fastq                   
├── Reference
│   └── hg19_download.sh
├── bins    
│   └── sentieon-genomics-201808.tar.gz
└── README.md

Installation

git clone https://github.com/shanghungshih/sentieon.git

Before you start

  1. decompress sentieon bin file
tar zxvf sentieon-genomics-201808.tar.gz

  1. download reference and annotation data (recommad using screen rather than bg or &)

    • open new screen : screen -S download_hg19, and run bash hg19_download.sh, then ctrl+A+D to detach
    • attach existed screen : get screen id with screen -ls, and screen -r xxx to attach, then ctrl+A+D to detach
    • close existed screen : get screen id with screen -ls, and screen -r xxx to attach, then ctrl+D to close it

  2. check sentieon/Jobs/variant_calling.sh, the followings are default setting:

    • SENTIEON_LICENSE : export SENTIEON_LICENSE=xxx.xxx.xxx.xxx:xxx
    • main directory : main_dir="/home/shanghung/sentieon"
    • fastq1 file name : fastq_1="${fastq_folder}/${SampleName}_R1.fastq.gz"
    • fastq2 file name : fastq_2="${fastq_folder}/${SampleName}_R2.fastq.gz"
    • number of threads : nt=32
    • update annotation files

  3. check sentieon/Jobs/run_Jobs.pl for changing max parallel numbers (depend on the total threads and $nt you set):

    • line36 : $running_job < 2

  4. put raw data of the sample to sentieon/Fastq in corresponding folder

  5. finally, run "one" sample before multiple submit for building reference index

Quick start

  1. run jobs (suggest running via screen)
    • -i : ID-File: the File contain Sample ID
    • -s : Start: From which lines (sample).
    • -e : End: To which lines (sample).
perl run_Jobs.pl -i test_list.txt -s 1 -e 1
  1. check jobs (if checkpoint found in Outputs, then return success)
    • list_ID : read from command line
    • checkpoint : "*.vqsr_SNP_INDEL.VQSR.pdf" (default)
bash check_Jobs.sh test_list.txt