Requirement of genotypic data for intermidiate generations

[yan-cheng-lin]

Hello,

It seems that the genotypic data of the intermidiate generations is essential for the analysis.
I'm interested in your program, however, I did not have any genotypic data of the intermidiate generations (G1-G3).
I have only genotypic data of founders and final DH lines.
Can I create sudo-parents with missing genotypic data instead?

Best regards,
YCL

[GoliczGenomeLab]

Dear @yan-cheng-lin,

Apologies for the late reply.

haploMAGIC was designed for detecting crossovers that occurred in specific meiotic events by comparing the parental genotypic sequences that recombined with the offspring sequence resulting from recombination events during meosis. So yes, unfortunately for you, haploMAGIC demands full pedigree and SNP sequence of all the individuals of the families (in your case, G0-G3) to be analyzed.

What is your population design? MAGIC or do you have the same common parent (NAM)?

Currently, I am working on a new tool that compares the last generation and the first generation inbred lines, that is the RILs/DHs and the founder lines, builds haplotype blocks and detects recombination events. I think that would be of interest for you.

All best,
@jamonterotena

[yan-cheng-lin]

Hello @jamonterotena,

Thank you for your reply, and also sorry for my late reply.
The population is a eight founder MAGIC DH populations from funnel crossing design.

Currently, I had reconstructed the founder haplotype mosaic by hidden markov model.
However, due to the genotyping error and lack of polymorphism between some founders, the estimation of recombination would be quite bias, if I counted directly from the changing of haplotypes along chromosome.
Your new tool that compares directly from the last generation and the founder for recombination estimation would be interesting. I am looking forward to it.

Best regards,
YCL

[GoliczGenomeLab]

Dear @yan-cheng-lin,

I just uploaded haploRILs. I hope they can help you with your task 😃

Please, let me know if you have any issue using the code or suggestion for improvement. Also, I will probably add new functionalities regarding your struggle with lack of polymorphism, so stay updated about the latest versions!

Best regards,
@jamonterotena

[yan-cheng-lin]

Hi @jamonterotena,

Thanks for the updated, that looks great.
I already tried out haploRILs this morning.
The functions works for my data. (but I have to modify the path for the haploRILs_function.R)

I would like to ask for your opinion about the parameter setting {nSnp} {step} {K}.
I have 2.7M SNP in total, but I guess it would be better to use the subset ~50K SNP. And compare the stability of the results.
Thus, what values would you recommend to use with ~50K SNP for 10 chromosomes of maize dataset?

P.S. I got a lot of warning messages when running the code, maybe you can check for it.
"summarise() has grouped output by 'id', 'nSnp', 'K', 'blocksFiltered'. You
can override using the .groups argument."

Best regards,
Yan-Cheng

[GoliczGenomeLab]

I replied on the haploRILs issues section!