The problem of linkage map larger than 1000 cm

[Birgül Güden]

Dear,

I'm new to R/qtl and i need some help. I filtered my markers with R and then used ICImap. My population RIL and ICIMap determined my cM values ​​are more than 1000 cM for each chromosome. By the way, I apologize for my English. I would be glad if you could help me.

[Karl Broman]

I can’t help with ICImap, but when I see big expansions in map length, I first look at whether it is due to a few intervals that are really large (which might indicate individual markers that are problematic) or is more widespread. If there are widespread expansions, you might look at whether the genotypes have been coded properly.

karl

[Birgül Güden]

I was very happy that you responded so quickly. Thank you very much. Is there a way I can convert it to cm in R?

5 Mayıs 2025 Pazartesi tarihinde saat 19:24:54 UTC-5 itibarıyla Karl Broman şunları yazdı:

[Karl Broman]

I don’t understand what you are trying to do.

karl

[Birgül Güden]

Let me explain immediately. 

Allele frequency 5%
Heterozygous rate <5%
Minor allele frequency > 5%
Monomorphic markers deleted

After doing these operations, I had 7800 SNPs left. In the next step, I first made my marker binning and order in ICIMap. The cM in the data I received from here is higher than 1000. What alternative can I use instead of ICIMap in R?
I checked my data, there are widespread expansions

5 Mayıs 2025 Pazartesi tarihinde saat 19:32:27 UTC-5 itibarıyla Karl Broman şunları yazdı:

[Karl Broman]

R/qtl has a function est.map() for re-estimating inter-marker distances.

karl