how to create new file
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1
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5.9 years ago
forever ▴ 80

Hi, I have the below large data:

100 100 rs2236941 A A

100 100 rs2236985 G G

100 100 rs2237142 C C

100 100 rs2237162 A G

100 100 rs2237175 A G

I need to create new line like

100 100 0 0 -9  A A G G C C A G A G

I appreciate any help? Regards

r • 1.1k views
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5
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You're going to need to provide rather more details (e.g., WTF is the -9?). Also, what have you tried?

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2
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This lgen file format:

100 100 rs2236941 A A

100 100 rs2236985 G G

100 100 rs2237142 C C

100 100 rs2237162 A G

100 100 rs2237175 A G

and this is ped file format:

100 100 0 0 -9 A A G G C C A G A G

I try to use plink --lfile Plate3_final_report --recode

But I got error:

Duplicate ID '100 100'
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2
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You still didn't explain what -9 is, probably unknown phenotype. In addition, the error message is quite clear. You cannot have duplicate IDs for a sample.

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