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Full Discussion: Simple sort with header
Top Forums Shell Programming and Scripting Simple sort with header Post 302424901 by durden_tyler on Wednesday 26th of May 2010 02:02:16 PM
Old 05-26-2010
If your file isn't tab delimited then:

Code:
$
$
$ cat f2
 CHR          SNP         BP   A1      C_A      C_U   A2        CHISQ            P           OR
  19   rs10401969   19268718    C      222      890    T      0.03462       0.8524       0.9857
   1   rs10873889   76734548    G      934     3811    A       0.5325       0.4656       0.9691
   1   rs11589059  214196749    C      271     1084    T      0.01928       0.8896       0.9902
$
$
$ gawk 'NR==1; {if(NR > 1) {print $0 | "sort -nk 8,8"}}' f2
 CHR          SNP         BP   A1      C_A      C_U   A2        CHISQ            P           OR
   1   rs11589059  214196749    C      271     1084    T      0.01928       0.8896       0.9902
  19   rs10401969   19268718    C      222      890    T      0.03462       0.8524       0.9857
   1   rs10873889   76734548    G      934     3811    A       0.5325       0.4656       0.9691
$
$

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LEARN ABOUT DEBIAN

vcf-isec

VCF-ISEC(1)							   User Commands						       VCF-ISEC(1)

NAME

       vcf-isec - create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files

SYNOPSIS

       vcf-isec [OPTIONS] file1.vcf file2.vcf ...

DESCRIPTION

       About: Create intersections, unions, complements on bgzipped and tabix indexed VCF or tab-delimited files.

	      Note that lines from all files can be intermixed together on the output, which can yield unexpected results.

OPTIONS

       -C, --chromosomes <list|file>
	      Process the given chromosomes (comma-separated list or one chromosome per line in a file).

       -c, --complement
	      Output positions present in the first file but missing from the other files.

       -d, --debug
	      Debugging information

       -f, --force
	      Continue even if the script complains about differing columns.

       -o, --one-file-only
	      Print only entries from the left-most file. Without -o, all unique positions will be printed.

       -n, --nfiles [+-=]<int>
	      Output positions present in this many (=), this many or more (+), or this many or fewer (-) files.

       -p, --prefix <path>
	      If present, multiple files will be created with all possible isec combinations. (Suitable for Venn Diagram analysis.)

       -t, --tab <chr:pos:file>
	      Tab-delimited file with indexes of chromosome and position columns. (1-based indexes)

       -w, --win <int>
	      In  repetitive  sequences, the same indel can be called at different positions. Consider records this far apart as matching (be it a
	      SNP or an indel).

       -h, -?, --help
	      This help message.

EXAMPLES

	      bgzip file.vcf; tabix -p vcf file.vcf.gz bgzip file.tab; tabix -s 1 -b 2 -e 2 file.tab.gz

vcf-isec 0.1.5							     July 2011							       VCF-ISEC(1)
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