Question: Conversion Of Ped/Map Or Bim/Bim/ Fam Files To Dosage For Gwas Mit Probable And Comparison With Imputated Genotypes
1
gravatar for mathias.gorski
6.0 years ago by
mathias.gorski20 wrote:

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 beeing compatible with former analysis it must unfortunatly be ProbABEL). For doing this I want to convert my ped/map files to dosage (.dose) format, but havent 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, thats 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

ADD COMMENTlink modified 6.0 years ago by zx87546.8k • written 6.0 years ago by mathias.gorski20
2
gravatar for zx8754
6.0 years ago by
zx87546.8k
London
zx87546.8k wrote:

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, ...)
ADD COMMENTlink written 6.0 years ago by zx87546.8k

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!

ADD REPLYlink written 5.6 years ago by ellens210
1

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

ADD REPLYlink written 5.6 years ago by zx87546.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1282 users visited in the last hour