Preliminary list of codes that need to be placed:
In this repository, you will find the pipeline scripts for the following:
In the Mitochondrial Analysis folder
- Calling and Filtering Variants in the Mitochondria --added
- Quantification of Mitochondrial Copy Number --added (may need to delete this, since it's not in paper?)
- Phylogeny using Mitochondrial Variants --added
- Plot of Spread of Mitochondrial haplotypes across Tasmania --combine with the nuclear genome maps.
- Should we include the Forestier and West Pencil Pine analysis? If at all, it should be in the supplementary?
In the Nuclear Genome Analysis folder
- Calling and filtering of variants from the nuclear genome--added but will need to join into single variant calling pipeline script
- Calling copy numbers on low-coverage samples
- Generating Phylogeny using SNVs from the Nuclear Genome + somatic mitochondrial variants
- QC and filtering the initial 600 probe panel (MIPs)
- Filtering of MIPs (post-QC) and overlapping with copy number states
- Generating Phylogeny using MIPs
- Telomere analysis
- Plotting spread of different groups across Tasmania