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Hello, I was wondering whether any adjustments to the HapNe-IBD algorithm are needed to make it compatible with local ancestry filtered IBD segments? I'm imagining using the browning pipeline for ASIB…
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The `SegSiteStructure` objects (defined [here](https://github.com/DanielSeidman/MutationScripts/blob/be44de33dcebcafa04677a3f711e6911a98137dc/MutationCaller3.py#L160)) look like they're intended to ho…
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Does your program output all of the IBD segments? I am curious about the parameter. Is this parameter designed to manage memory and runtime resources? Could using too small of a value for this parame…
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All three of these methods rely on an object called `ancestor_map` (C codebase) or `A` (Python mockups) to store segments that descend from each ancestral node in the tree sequence. In the case of `ib…
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`find_ibd` relies on creating 'master' lists of segments underneath ancestral node. However, these lists can take up a lot of memory, especially if they are high up in the tree.
However, it isn't …
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Assuming that we agree on filtering candidate segments based on the ``among`` and ``between`` segments within the IBD finding algorithm as proposed in #1662, the interface between the IBD finding and …
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Might as well document ``tsk_table_collection_ibd_segments`` and associated structs while our heads are in it. Probably worth doing the ``tsk_table_collection_find_ibd`` which takes a function pointer…
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The MRCA definition of IBD is useful in some cases, and it would be good for us to support it.
From an API perspective, I think all that we need to do is provide a ``definition="path"|"mrca"`` opti…
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Copied from Slack:
![comparison-ibd-binned-1cM](https://user-images.githubusercontent.com/17755074/127788948-6db42d7b-d6af-432a-8df7-e7aabb9a7f7f.png)
> Hi Yan and Jerome, I wanted to talk more ab…
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We are unclear on is how to move from phased haplotypes -> ibd tracts -> ibd sharing matrix. We understand the latter is what’s required to run the program (as a .sims file). We also know you provide …