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Dear all,
For my Anopheles gambiae project, I am using a constant recombination rate per-base set at 2.4.10^-8.
The manual does not indicate the unit behind the hc value, which is set to 0.05 b…
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### What's the new feature?
Sub task of #71
- ~~1-Tree (a.k.a. LittererLyons) recombination. Refs: [Litterer & Lyons 2012](https://arxiv.org/abs/1008.4942v2) and [Tchernychova 2015 Chapter 3.2 A…
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Just adding this (obvious) issue so that we have somewhere to keep track of this discussion on this. Perhaps @awohns can add a little explanation about what the critical sticking points are?
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Thank you very much for your excellent tool. You and Li mentioned that in the calculation of PSMC, there are two key parameters, parapattern and maxt, which need to be adjusted according to the actu…
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Hello,
Is there a way to have the positions where QUILT has decided to switch from one haplotype in the reference set to another? And to tell which of the reference haplotypes are chosen?
My dat…
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Would it be possible to have SINGER output the "full ARG" with marked recombination nodes (similar to that from msprime)? This would require maintaining unary nodes in the tree sequence, such as recom…
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Hi!
I used ReLERNN to estimate the recombination rate along a very long genome, and ran the analyses by pieces of 500Mb. The results between the different parts are comparable when I use the resu…
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We should change the ARG tutorial to say that _msprime_'s `record_full_arg` is now simply a shorthand for `additional_nodes = msprime.NodeType.COMMON_ANCESTOR | msprime.NodeType.RECOMBINANT`.
Addit…
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Hi there,
I've gotten markedly different results when phasing using pyrho maps compared to hapmap's lifted over maps. While looking for an explanation, I've noticed that the GRCh38 maps you've rele…