Revision: Recalculate EXTEND scores as re-assess at threshold

[sjspielman]

To assess the affects of tumor purity on our results, we should re-run the EXTEND score calculations, considering only samples that have tumor_fraction>= median tumor fraction (https://github.com/AlexsLemonade/OpenPBTA-analysis/pull/1622).

We should then assess how well the following results hold up:

• TERT and TERC correlations
  • https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/b0fdf6f24fe9c021f22e8b7da348708f68877ee5/content/03.results.md?plain=1#L208
• Aggressive vs. low-grade tumor trends
  • https://github.com/AlexsLemonade/OpenPBTA-manuscript/blob/b0fdf6f24fe9c021f22e8b7da348708f68877ee5/content/03.results.md?plain=1#L209