finna-be-octo-bear

GATK Workflow

• custom gatk workflow adopted from CIDR
• Modify to suit the setting at local servers

1. Install bwa, picard, and gatk in $HOME/bin
2. Download gatk_bundle files from GATK ftp sites in $GATK_RESOURCE_PATH
   • this includes reference genome (hg19), known indels, dbsnp138
3. set up bwa index
4. put fastq files in $PROJECT_FOLDER/$FASTQ_DIR
5. This script will create a subscript for each process in $SAMPLE/$SCRIPT
6. Change the number of threads to reflect your CPUs
7. Change the INPUT DATA below to match with your input