How to distinguish gene conversion from recombination?

[MapleLin-Bio]

Hi everyone!

I am trying to simulate tree sequence involving recombination and gene conversion events by setting the specific rate of both in msprime.sim_ancestry(). However, I cannot distinguish between breakpoints corresponding to recombination and gene conversion. I wonder if there is a way to solve this. I would appreciate it if you can help me!

Best regards,
Maple

[jeromekelleher]

I think you can do something by using the record_full_arg option and looking at the node flags, something like:

ts = msprime.sim_ancestry(
    3, sequence_length = 100, recombination_rate=0.003,
    gene_conversion_rate=0.002, gene_conversion_tract_length=5,
    random_seed=6, record_full_arg=True)
edges = ts.tables.edges[(ts.nodes_flags[ts.edges_child] & msprime.NODE_IS_GC_EVENT) > 0]
print(edges)

gives

╔══╤════╤═════╤══════╤═════╤════════╗
║id│left│right│parent│child│metadata║
╠══╪════╪═════╪══════╪═════╪════════╣
║0 │  58│   63│    22│   19│        ║
║1 │   0│   24│    27│   25│        ║
║2 │  26│   41│    27│   25│        ║
║3 │  43│   58│    27│   25│        ║
║4 │  63│  100│    27│   25│        ║
║5 │  41│   43│    28│   25│        ║
║6 │   0│   58│    29│   18│        ║
║7 │  63│  100│    29│   18│        ║
║8 │  24│   26│    29│   26│        ║
║9 │  41│   43│    30│   28│        ║
║10│   0│   24│    31│   27│        ║
║11│  26│   33│    31│   27│        ║
║12│  33│   41│    32│   27│        ║
║13│  43│   58│    32│   27│        ║
║14│  63│  100│    32│   27│        ║
╚══╧════╧═════╧══════╧═════╧════════╝

I think this gives the outbound edges from all GC events and the breakpoints will be somewhere in the left right coordinates. I'm not quite sure how you'd extract them though. You'd need to play with it a bit to see how it works, I think.

Hopefully this is a step in the right direction?