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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LEARN ABOUT REDHAT
unix2dos
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)