How can I convert .ped file to bed+bim+fam file using plink 1.9?
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2.0 years ago

I have a ped file for 50 samples. Also, I have map file for the same. How to make use of ped and map files to generate bed, bim and fam files ?

I tried running using plink,

./plink_1.9_linux_160914 --file input_files/50_samples.ped --make-bed --out 50_samples_try --noweb
PLINK v1.90b2i 64-bit (8 Sep 2014)         https://www.cog-genomics.org/plink2
(C) 2005-2014 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to 50_samples_try.log.
Note: --noweb has no effect since no web check is implemented yet.
15741 MB RAM detected; reserving 7870 MB for main workspace.
Error: Failed to open input_files/50_samples.ped.map. (--file expects a
filename *prefix*; '.ped' and '.map' are automatically appended.)

Please help

plink SNP next-gen gene ped • 3.4k views
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2.0 years ago
Nandini ▴ 900

Have you read the manual ?

The error you get "--file expects a filename prefix; '.ped' and '.map' are automatically appended." is self explanatory.

Please remove the prefix '.ped'

The command should be

plink --file 50_samples --make-bed --out 50_samples_try
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Thanks, But now am getting different error.

./plink_1.9_linux_160914 --file 50_samples --make-bed --out 50_samples_try

PLINK v1.90b2i 64-bit (8 Sep 2014)         https://www.cog-genomics.org/plink2
(C) 2005-2014 Shaun Purcell, Christopher Chang   GNU General Public License v3
Logging to 50_samples_try.log.
15741 MB RAM detected; reserving 7870 MB for main workspace.
Error: Failed to open 50_samples.map.
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Thanks Nandini Issue resolved :).

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