README.md

pdx-genome

Patient derived cancer xenograph genome analysis

1. Trimmomatic palindrome mode with high threshold (20)
2. Mapping paired end local alignment with either bwa-mem or bowtie2 to GRCh38_no_alt and GRCm38 preserving read order and only reporting one alignment per read.
3. Processing the mouse and human alignments with xenomapper (needs only python3 and a samtools binary in the path. Pip3 installable)
4. Samtools sort and index human reads

Using the human specific reads for:

5. Platypus mutation calling (tumour only)
6. Varscan mutation calling (tumour only)
7. Gridss
8. Annotation of variants with VEP including population variant frequencies (ExAC)

Instructions

1. Create a new empty directory to hold code, scripts and output
2. Clone this repository: git clone --recursive https://github.com/WEHI-ResearchComputing/pdx-genome Note the recursive argument to bring in the common tool definitions.
3. Create a python virtual enviroment to hold the software
   • module load python
   • virtualenv toil-env
   • . toil-env/bin/activate
   • pip install git+https://github.com/WEHI-ResearchComputing/wehi-pipeline
4. You should now be able to run the tests against the minimal data in the pdx-genome/data directory.
   1. Test with the CWL reference implementation
      • cd /path/to/pdx-genome
      • mkdir test
      • cd test
      • cwltool ../src/pdx-scatter.cwl ../src/pdx-inp.yml
   2. Test with Toil. Inspect the runall.sh script and make sure the directories are correct.