VCFtools BEDtools compare, intersect, merge

A Good computational biologist is only as good as the tools he uses (or maybe how good he is at google) rofl kidding ...
Life is always easier when you find the correct tool.
I also adopt the path of least resistance when trying to solve problems that are more common than I imagine.
There's always the good old linux tools for comparing SNPs called from different programs / options

   grep | sed | awk | cut | diff | comm
   see http://ged.msu.edu/angus/tutorials-2011/snp_tutorial.html


and if you are working with NGS data, you most probably already have samtools installed on your system and you might have used bcftools
Did you also know that there's also a (unrelated) set of tools called vcftools?
http://vcftools.sourceforge.net/

The VCFtools package is broadly split into two sections: 

• The vcftools binary program, generally used to analyse VCF files.
• The Vcf.pm perl module, which is a general Perl API containing a core of the utilities vcf-convert, vcf-merge, vcf-compare, vcf-isec, and others.

  Documentation

  • Documentation for the binary executable vcftools
  • The Perl API and scripts
  • Useful shell one-liners

  Examples of usage by topic

  • Installation
  • Annotating
  • Comparing
  • Concatenating
  • Converting
  • Intersections, complements
  • Merging
  • Querying
  • Reordering columns
  • Stats
  • Stripping columns
  • Useful shell one-liners
  • Validating

Then there's  also the highly used BEDTools http://code.google.com/p/bedtools/

which I highly recommend to keep as part of your tools collection. Check out the link below

Do watch out for this 'oversight' in vcftools as pointed out in seqanswers.
Overlap number discrepancy between VCFTools and BEDTools

Usage

Examples of common usage.   Featured

Sequence Variant Analyzer SVA

The rapidly evolving high-throughput DNA sequencing technologies have now allowed the fast generation of large amount of sequence data for the purpose of performing such whole-genome sequencing studies, at a reasonable cost. S equence V ariant A nalyzer, or SVA , is a software tool that we have been developing to analyze the genetic variants identified from such studies.

SVA is designed for two specific aims:

(1) To annotate the biological functions of the identified genetic variants, visualize and organize them;
(2) To help find the genetic variants associated with or responsible for the biological traits or medical outcomes of interest.

SVA is:
a program designed to run on a LINUX platform, with a graphical user interface (GUI), meaning that the main functions of this program can be done with clicking buttons.

a program specifically designed for analyzing genetic variants that have already been called (identified) from a whole genome sequencing study. So do not try to find a function here to align short reads and call variants - SVA is not designed for those purposes - many other software tools, for example, BWA and SAMTOOLS , were developed for those purposes.

How it  works

Dleon highlights tools worth a mention at ABRF 2010

from Dleon

Some of these are new to me as well!

excerpt
GNomEx:
It is a a web accessible database and LIMS to organize and track the generation of raw genomic data and associated downstream analysis.
https://hci-as1.hci.utah.edu/gnomex/gnomex.html

GenoPub:
It is a Genomic Annotation Publisher which stores information about each annotation in a database. http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2

Intergrative Genome Browser:
The Integrated Genome Browser is an interactive, zoomable, scrollable software program you can use to visualize and explore genome-scale data sets, such as tiling array data, next-generation sequencing results, genome annotations, microarray designs, and the sequence itself.
http://www.bioviz.org/igb/

Galaxy:
Galaxy allows you to do analyses without the need to install or download software. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples, etc.
http://main.g2.bx.psu.edu/