Convert IMPUTE2 into the files that ProbABEL can read

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ljiang
Posts: 1
Joined: Thu Jun 09, 2016 10:10 pm

Convert IMPUTE2 into the files that ProbABEL can read

Postby ljiang » Thu Jun 09, 2016 10:20 pm

Hi,

I have imputed dataset from IMPUTE2, including .info, .info_by_sample, and .txt.gz (contains the genotype data) files. I would like to know how I can convert these data files into the .mlinfo and .mldose files. I tried to use the package in R (DatABEL) to convert the .txt.gz file into the filevector format. After 20 minutes, it gave me an error as:

Code: Select all

Error in (function (cl, name, valueClass)  :
  assignment of an object of class “NULL” is not valid for @‘data’ in an object of class “databel”; is(value, "externalptr") is not TRUE

I am wondering if there are other tools that I can use to generate the .mldoes files. Moreover, I would like to know how to generate the .mlinfo file from the IMPUTE2 data.I assume that the "info" in IMPUTE2 corresponds to the "Rsq" in .mlinfo and "certainty" in IMPUTE2 corresponds to the "Quality" in .mlinfo. However, I don't know where I can find the allele information (A1, A2).

Thank you so much!

Sincerely,
Lai Jiang.
Last edited by lckarssen on Sat Jun 11, 2016 7:19 pm, edited 1 time in total.
Reason: Reformatted output with the [code] tag

lckarssen
Site Admin
Site Admin
Posts: 321
Joined: Tue Jan 04, 2011 3:04 pm
Location: Utrecht, The Netherlands

Re: Convert IMPUTE2 into the files that ProbABEL can read

Postby lckarssen » Mon Jun 13, 2016 8:38 am

Hmm, that's strange. I thought we already squashed that bug a long time ago. Which version of DatABEL are you using? And do you have GenABEL installed? If so, which version?
How many individuals and variants do you have?
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Lennart Karssen
PolyOmica
The Netherlands
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