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popgenmethods / pyrho

Fast inference of fine-scale recombination rates based on fused-LASSO
MIT License
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Identical recombination rates in chromosomal plots #32

Open jbernst opened 6 months ago

jbernst commented 6 months ago

Hello,

I am running pyrho v0.1.7 to get recombination rates of hybrid species and their parentals. We are using whole genome resequencing data (vcf files of biallelic SNPs), with 25 individual. The analysis ran smoothly, and this is actually the second time we are running the analysis after having to change some of our data. The first time we ran pyrho, we saw no issues with plotting recombination rates. However, upon rerunning our analysis we are now seeing segments of chromosomes that look like they have identical recombination rates (that we were not seeing before), showing up as horizontal lines in the plots (see attached image). What could be causing these? It doesn't seem to be due to missing data as we having plenty of SNPs in these regions.

If there is anything else needed, please let me know. This is my first time running pyrho, so my apologies if I forgot any crucial information.

Thank you!

image

jeffspence commented 6 months ago

Hi @jbernst -- sorry for the slow response. Those definitely look a bit odd, but nothing obvious springs to mind to explain them. Are all of the SNPs in those regions low frequency (e.g., singletons)? Or do they look odd in some other respects (e.g., high degree of missingness, unusually low SNP density, etc...)? The fact that they're toward the beginning and end of the scaffold makes me wonder if the data are a bit weird there (e.g., close to a telomere or centromere). Sorry that I can't be more helpful, but my first guess would be some kind of data issue or interaction between something weird with the data and pyrho.