Using ATGC genotype format

[Akinlade Oluwaseun Johnson]

Hi,

I am trying to use QTL2 for a MAGIC population developed from 8 founders but my genotype file is in ATGC format. Is it possible to use this format? Secondly, I do not have the genetic map I only have physical map, is it possible to run the analysis with just the physical map?

Thank you and best regards,

Olujohnson 

[Karl Broman]

Yes, it needs to be converted from ATGC to like A/H/B or 1/2/3.

For qtl analysis, you ultimately need an estimate of a genetic map, but you could start by using the physical map in Mbp, or use some estimate of the recombination rate to convert Mbp to cM.

karl

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[Olujohnson]

Thank you so much, Karl.

I will give it a try and update the group on my progress.

Please is there any function in qtl2 to estimate the recombination rate?

Thank you and best regards,

olujohnson

[Karl Broman]

You can use the function est_map() to estimate the inter-marker distances.

Here's an example for the 19-way Arabidopsis MAGIC lines.

library(qtl2)
file <- paste0("https://raw.githubusercontent.com/rqtl/",
               "qtl2data/main/ArabMAGIC/arabmagic_tair9.zip")
arab <- read_cross2(file)

map <- est_map(arab, quiet=FALSE) # can use cores=0 to use multiple CPU cores

arab$gmap <- map

It may take a super long time.

karl

[Olujohnson]

Thank you so much, Karl.