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Full Discussion: How to use the join command to obtain tab delimited text files as an output?
Top Forums UNIX for Dummies Questions & Answers How to use the join command to obtain tab delimited text files as an output? Post 302659231 by Corona688 on Wednesday 20th of June 2012 03:10:20 PM
Old 06-20-2012
Code:
$ man join

JOIN(1)                          User Commands                         JOIN(1)



NAME
       join - join lines of two files on a common field

SYNOPSIS
       join [OPTION]... FILE1 FILE2

DESCRIPTION
       For  each  pair of input lines with identical join fields, write a line
       to standard output.  The default join field is the first, delimited  by
       whitespace.  When FILE1 or FILE2 (not both) is -, read standard input.

       -a FILENUM
              print  unpairable  lines coming from file FILENUM, where FILENUM
              is 1 or 2, corresponding to FILE1 or FILE2

       -e EMPTY
              replace missing input fields with EMPTY

       -i, --ignore-case
              ignore differences in case when comparing fields

       -j FIELD
              equivalent to `-1 FIELD -2 FIELD'

       -o FORMAT
              obey FORMAT while constructing output line

       -t CHAR
              use CHAR as input and output field separator


...

This User Gave Thanks to Corona688 For This Post:
evelibertine
 

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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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