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Full Discussion: PLINK help
Top Forums Shell Programming and Scripting PLINK help Post 302694773 by smitra on Friday 31st of August 2012 11:32:36 AM
Old 08-31-2012
PLINK help

Hi Plink users,
I am very new in GWAS and decided to use PLINK for this. But I am struggling with file formats.
I have one exome data with 200000 SNPs in it. But it is in .txt format. But all the necessary fields are there in different columns.
Can you please suggest me how I can create the plink .bed file?
Is there any direct way to create .bed file from .txt?

I tried to create a .bim and a .fam file following the instruction in PLINK website Binary files (BED/BIM/FAM)
Is there any way to create .bed file from these two (.bim & .fam) files?
Please let em know.
Thanks a lot,
Suparna.
 

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unix2dos(1)						      General Commands Manual						       unix2dos(1)

NAME
unix2dos - UNIX to DOS text file format converter SYNOPSYS
unix2dos [options] [-c convmode] [-o file ...] [-n infile outfile ...] Options: [-hkqV] [--help] [--keepdate] [--quiet] [--version] DESCRIPTION
This manual page documents unix2dos, the program that converts text files in UNIX format to DOS format. OPTIONS
The following options are available: -h --help Print online help. -k --keepdate Keep the date stamp of output file same as input file. -q --quiet Quiet mode. Suppress all warning and messages. -V --version Prints version information. -c --convmode convmode Sets conversion mode. Simulates unix2dos under SunOS. -o --oldfile file ... Old file mode. Convert the file and write output to it. The program default to run in this mode. Wildcard names may be used. -n --newfile infile outfile ... New file mode. Convert the infile and write output to outfile. File names must be given in pairs and wildcard names should NOT be used or you WILL lost your files. EXAMPLES
Get input from stdin and write output to stdout. unix2dos Convert and replace a.txt. Convert and replace b.txt. unix2dos a.txt b.txt unix2dos -o a.txt b.txt Convert and replace a.txt in ASCII conversion mode. Convert and replace b.txt in ISO conversion mode. unix2dos a.txt -c iso b.txt unix2dos -c ascii a.txt -c iso b.txt Convert and replace a.txt while keeping original date stamp. unix2dos -k a.txt unix2dos -k -o a.txt Convert a.txt and write to e.txt. unix2dos -n a.txt e.txt Convert a.txt and write to e.txt, keep date stamp of e.txt same as a.txt. unix2dos -k -n a.txt e.txt Convert and replace a.txt. Convert b.txt and write to e.txt. unix2dos a.txt -n b.txt e.txt unix2dos -o a.txt -n b.txt e.txt Convert c.txt and write to e.txt. Convert and replace a.txt. Convert and replace b.txt. Convert d.txt and write to f.txt. unix2dos -n c.txt e.txt -o a.txt b.txt -n d.txt f.txt DIAGNOSTICS
BUGS
The program does not work properly under MSDOS in stdio processing mode. If you know why is that so, please tell me. AUTHOR
Benjamin Lin - ( blin@socs.uts.edu.au ) MISCELLANY
Tested environment: Linux 1.2.0 with GNU C 2.5.8 SunOS 4.1.3 with GNU C 2.6.3 MS-DOS 6.20 with Borland C++ 4.02 Suggestions and bug reports are welcome. SEE ALSO
dos2unix(1) 1995.03.31 unix2dos v2.2 unix2dos(1)
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