Genetic map construction

[Madi Shoken]

Hello,

How to filtered genotypic data to remove markers with >10% missing data, with <0.1 minor allele frequency, and markers with distorted segregation?

Regards, 

Madi

[Karl Broman]

It depends very much on the type of cross. What data are you considering?

Also, see the tutorial about genotype diagnostics in diversity outbred mice:

https://kbroman.org/qtl2/assets/vignettes/do_diagnostics.html

karl

[Karl Broman]

I think look at n_missing, calc_geno_freq, and calc_raw_geno_freq.

https://search.r-project.org/CRAN/refmans/qtl2/html/n_missing.html

https://search.r-project.org/CRAN/refmans/qtl2/html/calc_geno_freq.html

https://search.r-project.org/CRAN/refmans/qtl2/html/calc_raw_geno_freq.html

karl

[Madi Shoken]

Cross type is wheat RILs at F7 and the data is its genetic map. Thanks for the link, just found and working on it, but could not find the way for detecting distorted markers or did I miss the function?.

Madi

сб, 4 мая 2024 г., 16:18 Karl Broman <kbr...@gmail.com>:

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