Conversion Of Ped/Map Or Bim/Bim/ Fam Files To Dosage For Gwas Mit Probable And Comparison With Imputated Genotypes

Question

[mathias.gorski]

Hi all,

the title says it all: I have plink compatible ped/map (bim/bam/fam) data and want to compare this genotype data with imputed data and I also want to do linear and logistic regression analysis with ProABEL (for being compatible with former analysis it must unfortunately be ProbABEL). For doing this I want to convert my ped/map files to dosage (.dose) format, but haven't found a tool, that can do this automatically. Scripting it by hand will cost me days. Do you know of any tool, that can convert from ped to dose?

btw, I know, that the dosages, that will be outputted can only be concrete numbers 0,1,2, that's ok. Furthermore I know f. e. gtool (http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html), but it converts to file format compatible with Impute and SNPtest only.

Thank you all in advance, any hint is helpful :)

Best,
Matthew

Answer 1

[zx8754]

Use GTOOL to convert PEDMAP to GEN format:

gtool -P --ped example/example.ped --map example/example.map --og example/out.gen --os example/out.sample

Then use GenABEL to convert GEN format to MACH format:

impute2mach(genofile, infofile, samplefile, machbasename, maketextdosefile = TRUE, ...)

[ellens2]

Hello, I'm trying to do the same thing as Mathias. But when I run gtool, I get only a samplefile and genofile out. I can't find on google what the infofile should look like. Do you know that the infofile should look like? Thanks!

[zx8754]

See http://mathgen.stats.ox.ac.uk/impute/output_file_options.html