\name{callSNPs}
\alias{callSNPs}
\title{Finding Single Nucleotide Polymorphisms (SNPs) from next-gen sequencing data}
\description{Use read coverage and allele frequency to call SNPs}
\usage{
callSNPs(SAMfile,readLength,refGenomeFile,outputFile,minReadCoverage=5,minAlleleFraction=0.5)
}
\arguments{
  \item{SAMfile}{ a character string giving the name of a SAM format file.}
  \item{readLength}{ a numeric value giving the read length.}
  \item{refGenomeFile}{ a character string giving the name of a FASTA format file which contains reference sequences.}
  \item{outputFile}{ a character string giving the name of the output file which includes discovered SNPs.}
  \item{minReadCoverage}{ a numeric value giving the minimal number of reads which cover a chromosomal location, when considering if it contains a SNP or INDEL. 5 by default.}
  \item{minAlleleFraction}{ a numeric value giving the minimal fraction of reads which supports the called SNP or INDEL, out of all the reads which cover that chromosomal location. 0.5 by default.}
  }
\details{
This function takes as input a SAM format file, which includes mapping results for a set of reads, and then calls SNPs using read coverage and allele frequency for each chromosomal location.\\

It requires the chromosome names included in the SAM file to be 'chr1', 'chr2', 'chr3', ..., 'chrX', and 'chrY'.\\ 

To be reported as a SNP-containing loci, a chromosomal location must be covered by at least \code{minReadCoverage} reads and the fraction of reads, which include bases different from the reference base at that location, must be equal to or greater than \code{minAlleleFraction}.

}
\value{
A text file including detailed information about called SNPs, such as chromosomal location, reference base, alternative base, read coverage, allele frequency and so on. 
}
%\references{
%}
\author{Wei Shi and Jenny Zhiyin Dai}
%\note{}
%\seealso{}
\examples{}
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