Search results

update inference script

Status: Open.

#72 In HighlanderLab/tree_seq_pipeline;

· gmafrafortuna opened on Jan 12, 2024

improve testing

Status: Open.

#70 In HighlanderLab/tree_seq_pipeline;

· hannesbecher opened on Dec 1, 2023

Remove print statements

Status: Open.

#65 In HighlanderLab/tree_seq_pipeline;

· gmafrafortuna opened on Nov 21, 2023

Move ancestral inferrence after the merge

Status: Open.

#61 In HighlanderLab/tree_seq_pipeline;

· janaobsteter opened on Nov 17, 2023

Figure out how to add the pedigree to the inference

Status: Open.

#56 In HighlanderLab/tree_seq_pipeline;

· janaobsteter opened on Nov 17, 2023

Check sgkit documentation how to import a VCF file & how we will move towards using sgkit in this tree seq pipeline

Status: Open.

#55 In HighlanderLab/tree_seq_pipeline;

· gregorgorjanc opened on Nov 17, 2023

Add optional arguments to the add_populations function in the Prepare_samples.py

Status: Open.

#50 In HighlanderLab/tree_seq_pipeline;

· janaobsteter opened on Nov 17, 2023

Modify the ancestral inference to be able to infer on per-chromosome basis

Status: Open.

#46 In HighlanderLab/tree_seq_pipeline;

· janaobsteter opened on Nov 10, 2023

Move from samples file constructions to the new sgkit

Status: Open.

#43 In HighlanderLab/tree_seq_pipeline;

· janaobsteter opened on Nov 9, 2023

Add dating scripts to the pipeline

Status: Open.

#42 In HighlanderLab/tree_seq_pipeline;

· janaobsteter opened on Nov 9, 2023

How to handle chromosome names?

Status: Open.

#41 In HighlanderLab/tree_seq_pipeline;

· janaobsteter opened on Nov 9, 2023

Add benchmarking to the rules

Status: Open.

#40 In HighlanderLab/tree_seq_pipeline;

· janaobsteter opened on Nov 9, 2023