Hello,
I have a clonally propagating fungus that I am resequencing from different geographic locations. Since it is thought to be clonal, I expect very little or no recombination happening, nevertheless I want to test for that.
Challenges that I have is that it is a tetraploid, so I cannot simply align contigs and look for recombination. What I think I need to do is call variants and then try to phase them into blocks. I have been successful at doing that, and now I have a VCF file with phased data.
But now I have no idea what software I can use that to look for recombination. In principle I understand how it should work. I have several isolates with phased variants. I know most of these variants are shared among isolates, it makes sense since it is clonal. So now, if variants share the same phase from isolate to isolate, then there is no putative crossover. However if one isolate has a different phase, then that could potentially hint at a recombination event.
I have managed to phase my data with HapCompass.
Let me know if you have any ideas.
Thank you,
Adrian
I have a clonally propagating fungus that I am resequencing from different geographic locations. Since it is thought to be clonal, I expect very little or no recombination happening, nevertheless I want to test for that.
Challenges that I have is that it is a tetraploid, so I cannot simply align contigs and look for recombination. What I think I need to do is call variants and then try to phase them into blocks. I have been successful at doing that, and now I have a VCF file with phased data.
But now I have no idea what software I can use that to look for recombination. In principle I understand how it should work. I have several isolates with phased variants. I know most of these variants are shared among isolates, it makes sense since it is clonal. So now, if variants share the same phase from isolate to isolate, then there is no putative crossover. However if one isolate has a different phase, then that could potentially hint at a recombination event.
I have managed to phase my data with HapCompass.
Let me know if you have any ideas.
Thank you,
Adrian
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