Loading IMPUTE2 dosage data into plink/seq
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Entering edit mode
6.5 years ago

Hi!

I'm trying to load the dosage data from IMPUTE2.

It keeps giving me this error 

pseq error : invalid dosage line entry, wrong number of rows

I even tried to work with the mydata.dat example given on this site https://atgu.mgh.harvard.edu/plinkseq/dosage.shtml 

But then it gives me the same error 

pseq error : invalid dosage line entry, wrong number of rows (expecting 10 but found 1 ):

rs001  chr1  1000  A  C   0.1  1.2  0.0  1.6  2.0

 

Kindly help.

Thanks in advance.

plink/seq impute2 dosage • 2.0k views
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Entering edit mode
6.3 years ago
Vincent Laufer ★ 1.4k

Is the file space-delimited? did you try running the command on a tab-delimited file?

 

awk '{gsub(/ /,"\t"); print $0}' myfilename.txt > myfilename.tsv

 

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