Variant Pattern Analyzer

The package can be used to extract sequencing variants with user-specified frequency based on either variant calls alone or both variant and sequence calls in the next-generation sequencing study. To make use of sequence call data, the installation of open source tabix tool is required. Examples of using VPA can be found in doc/VPA.pdf. The manual can be downloaded here.

VPA use tabix function for efficient information retrieval (http://samtools.sourceforge.net/tabix.shtml). There are two ways to install tabix function:
a) To install tabix directly from SAMtools:

• URL: http://sourceforge.net/projects/samtools/files/tabix/
  
• Once installed, users can specify the path of tabix in the argument "tabix=" of the function LoadFiltering (or pos2seq).
  
• Note that tabix is only available for Unix-like operation system.
  

b) To install scanTabix from the latest version (>=1.6.0) of Rsamtools:

• URL: http://www.bioconductor.org/packages/2.9/bioc/html/Rsamtools.html
  
• Once installed and loaded (i.e., library(Rsamtools)), the function scanTabix in the package Rsamtools can be invoked by setting the argument "tabix=NULL" of the function LoadFiltering (or pos2seq).
  
• Note that scanTabix is available for both Unix-like and windows operation system.
  

We recommend users to install tabix directly from SAMtools as it runs more efficiently than Rsamtools in current version.

For Unix-like operation system, the version of R should be >= 2.12.1; For Windows operation system, the version of R should be >=2.14.0.
Within R:
> install.packages("VPA", repos=c("http://R-Forge.R-project.org", "http://cran.r-project.org"))
To run VPA package, it is required to have tabix installed (as described in the Dependencies section).

The project summary page you can find here.

Date: Wed Oct 12
version 0.3.2; Modified manual and vignette.
Date: Fri Sep 30
version 0.3.0.
Updata functions:
filtervcf, LoadFiltering: Add min, max for DP. Add alter.AD, cutoff for alt allele depth. Add alter.ADP, percentage of AD.
vcfreq: add genotype. change to allele frequency. add statistical test, fisher.test and chisq.test.
Add functions:
getref, Pos2Gene. Functions to map positions to genes.
filterpos: filter specified positions, such as dbSNP, 1K genome, customized vcf. Input file can be vcf, bed, gff and data.frame.
gefreq: calculate gene level frequencies between groups and annotate variants to genes.
Vignette:
Modified VPA.Rnw. Add a new section about dbSNP/1000Genome filtering. Add more arguments in functions.
Bugs fixed.
Date: Wed Aug 31
version 0.2.4.
Add PL to LoadFiltering and Patterning. Prossible variants can be filtered now.
Bugs fixed.
Date: Mon Aug 8 08:56:21 2011
version 0.2.2, pos2seq can choose Rsamtools instead of tabix
Date: Thu Jul 28
version 0.2.1. add REF and ALT to function vcfreq.

VPA: an R tool for analyzing sequencing variants with user-specified frequency pattern. Hu Q, Wang D, Yan L, Zhao H, Liu S. BMC Res Notes. 2012 Jan 14;5:31.