Walk through tutorial

Please install required dependencies and set up genome resource directory before running the pipeline.

1. Download and uncompress demo data at https://data.broadinstitute.org/Trinity/CTAT/mutation/ctat_mutation_demo.tar.gz Unzip folder.
2. Set up environment

   export GATK_HOME=/path/to/GATK
   export PICARD_HOME=/path/to/picard
   export CTAT_GENOME_LIB=/path/to/installed/ctat_genome_lib
   

3. Use the following command to run the pipeline:

   python ctat-mutations/ctat_mutations \
   --plot \
   --out_dir varcalling.outdir \
   --threads 8 \
   --variant_filtering_mode GATK \
   --left ctat_mutation_demo_1.fastq \
   --right ctat_mutation_demo_2.fastq \
   --variant_call_mode GATK \
   --tissue_type Other \
   --email <your_emai_id>
   

The main output of the pipeline is cancer.tab file. The demo data used here is