This PR adds logic to rerun the analysis pipeline using variants called in samples 004 and 005 after aligning to the human genome alone. Previously, all samples (regardless of PDX status) were aligned to both mouse and human genomes. A disambiguate step was applied following the dual alignment.
This PR analyzes samples 004 and 005 (which are human tumors) without alignment to the mouse genome. All figures and all results are updated to include variants called in these tumors in the "human-only" pipeline.
487228a adds a visualization of the difference between the disambiguate and human-only pipelines. For these two samples, there is not much difference.
This PR adds logic to rerun the analysis pipeline using variants called in samples
004and005after aligning to the human genome alone. Previously, all samples (regardless of PDX status) were aligned to both mouse and human genomes. A disambiguate step was applied following the dual alignment.This PR analyzes samples
004and005(which are human tumors) without alignment to the mouse genome. All figures and all results are updated to include variants called in these tumors in the "human-only" pipeline.487228a adds a visualization of the difference between the disambiguate and human-only pipelines. For these two samples, there is not much difference.