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Issues list

update inference script
#72 opened Jan 12, 2024 by gmafrafortuna
improve testing
#70 opened Dec 1, 2023 by hannesbecher
1 of 4 tasks
@hannesbecher
3
Remove print statements
#65 opened Nov 21, 2023 by gmafrafortuna
Move ancestral inferrence after the merge
#61 opened Nov 17, 2023 by janaobsteter
@janaobsteter
Figure out how to add the pedigree to the inference
#56 opened Nov 17, 2023 by janaobsteter
@AudreyAAMartin
1
Check sgkit documentation how to import a VCF file & how we will move towards using sgkit in this tree seq pipeline
#55 opened Nov 17, 2023 by gregorgorjanc
@AprilYUZhang
3
Add optional arguments to the add_populations function in the Prepare_samples.py
#50 opened Nov 17, 2023 by janaobsteter
Modify the ancestral inference to be able to infer on per-chromosome basis
#46 opened Nov 10, 2023 by janaobsteter
@janaobsteter
1
Move from samples file constructions to the new sgkit
#43 opened Nov 9, 2023 by janaobsteter
1
Add dating scripts to the pipeline
#42 opened Nov 9, 2023 by janaobsteter
1
How to handle chromosome names?
#41 opened Nov 9, 2023 by janaobsteter
@hannesbecher
2
Add benchmarking to the rules
#40 opened Nov 9, 2023 by janaobsteter
3
Do we need a step to move non-bialellic SNPs from the VCF?
#39 opened Nov 9, 2023 by janaobsteter
@janaobsteter
2
How to tell snakemake which one is the "main" file when merging
#29 opened Jul 4, 2023 by janaobsteter
@gmafrafortuna
Develop installation instructions/README
#5 opened Mar 24, 2023 by gregorgorjanc
1
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