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rqtl / qtl2

QTL analysis software for high-dimensional data and complex cross designs
https://kbroman.org/qtl2
GNU General Public License v3.0
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Genotype format conversion for multiparental MAGIC populations 123 #226

Closed jamonterotena closed 11 months ago

jamonterotena commented 11 months ago

I'm trying to prepare the genotyping data from a multiparental MAGIC population by applying the described format 123 for AA, AB, BB. I have a PED file with PLINK genotyping format 0 1, where 0 stands for minor and 1 for major allele.

I'm struggling to find any way that is already available to convert from this 'allele-by-column' format to a 'SNP-by-column' format, which would enable to produce the required format.

I would appreciate if you could share any help on this issue :)

kbroman commented 11 months ago

You can leave it coded that way, and indicate that encoding in the control file.

In genotypes, the example we have looks like this:

genotypes:
  - SS: 1
  - SB: 2
  - BB: 3

But you could instead put:

genotypes:
  - 0: 1
  - 1: 3

I prefer to have the github issues for problems with the software, and questions about its use at the R/qtl2 google group. If you can, please join the google group.