exactSNP: a SNP caller that discovers SNPs by testing signals against local background noises

exactSNP is a highly accurate and efficient program for detecting SNPs. It can be accessed from SourceForge Subread package or from Bioconductor Rsubread package. Both packages include a suite of programs for processing next-gen sequencing data.

Input and output

The input to exactSNP includes a SAM/BAM file and a FASTA file including reference sequences. exactSNP outputs a VCF format file that includes discovered SNPs.

Installation

To use exactSNP program included in the SourceForge Subread package, please download the package from SourceForge. After downloading, type the following command to uncompress it:

tar zxvf subread-1.x.x.tar.gz
Enter the src subdirectory under the home directory of this package and then issue the following command to build it on a Linux/unix computer:
make -f Makefile.Linux
To build it on a Mac OS X computer, issue the following command:
make -f Makefile.MacOS
If the package is successfully built, executables including the exactSNP program will be created in a subdirectory named 'bin' under the home directory of the package.

To use exactSNP program included in the Bioconductor R package Rsubread, you will need to have R installed on your computer. You can then install Rsubread package into your R. Please refer to Rsubread webpage for installation of the Rsubread package.

Example commands

Below is an example command for running exactSNP included in the SourceForge Subread package,

exactSNP -b -i mapping_results.bam -g mm10.fa -o calledSNPs.vcf

and below is an example command for running exactSNP included in the Bioconductor Rsubread package.

exactSNP(readFile="mapping_results.bam",isBAM=TRUE,refGenomeFile="mm10.fa",outputFile="calledSNPs.vcf")

Citation

Liao Y, Smyth GK and Shi W (2013). ExactSNP: an efficient and accurate SNP calling algorithm. In preparation

Users Guide

Type exactSNP to see the usage information, or have a look at the Subread User's Guide for more details (Chapter 6).

Get help

The best way to get help is to send your questions to the SEQanswers mailing list or the Bioconductor mailing list. Alternatively, you may directly contact Dr. Wei Shi (shi at wehi dot edu dot au).

Links

Subread: A superfast and accurate read aligner.

Subjunc: Detecting exon-exon junctions and mapping RNA-seq reads.

featureCounts: A read summarization program.

Rsubread: A bioconductor R package for read mapping, exon-exon junction detection and read summarization.

A case study for analyzing RNA-seq data: Using Bioconductor packages Rsubread and Limma to perform a complete analysis for RNA-seq data.

Subread package overview: Brief description to Subread package.