Loading IMPUTE2 dosage data into plink/seq

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

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.

plinkseq dosage impute2

• 3,100 views • link

updated 4.2 years ago by Ram

• written 11.2 years ago by potassiumiodide0990

1 answer

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

• 0 views • link

updated 4.2 years ago by Ram

• written 11.0 years ago by LauferVA

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