Select data set to run rufus warm-up on

[stefinfection]

Evaluate existing performance of RUFUS:

Option A

1. Find out sample IDs for PCAWG data used
2. Get bams and vcfs corresponding to those samples
3. Set up experimental design of N-T pairs
4. Run RUFUS on pairs
5. Accumulate calls and quantify sensitivity & non-overlapping calls (true positives?)
6. Generate figures to compare first round of PCAWG calls vs. my second round

[stefinfection]

Option B

1. Set up experimental design
2. Write up what we expect to see for results
3. Run RUFUS on hierarchical pairs
4. Analyze overlap with existing calls - what do existing calls look like? Is there a vcf somewhere?
5. Quantify sensitivity and non-overlapping calls
6. Generate figures to demonstrate overlap between existing calls and our calls + extra calls

NOTE: make sure to keep track of how long the runs take