NAME

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

USAGE

       exactSNP [options] -i input -g reference_genome -o output

       Required arguments:

       -i <file>
              Specify name of an input file including read mapping results. The

              [-b if BAM] format of input file can be SAM or BAM (-b needs to be specified

              if a BAM file is provided).

       -g <file>
              Specify name of the file including all reference sequences. Only one  single  FASTA
              format file should be provided.

       -o <file>
              Specify  name  of  the  output  file.  This  program outputs a VCF format file that
              includes discovered SNPs.

       Optional arguments:

       -a <file>
              Provide a set of annotated SNPs (e.g. SNPs included in  the  dbSNP  database).  The
              supplied  file  should be in VCF format. Providing known SNPs to the program should
              improve its SNP calling performance. Note that the provided SNPs may or may not  be
              called.

       -b     Indicate the input file provided via -i is in BAM format.

       -Q <int>
              Specify  the  q-value  cutoff  for  SNP  calling  at sequencing depth of 50X. 12 by
              default. The corresponding p-value cutoff is 10^(-1*Q).   Note  that  this  program
              automatically  adjusts the q-value cutoff according to the sequencing depth at each
              chromosomal location.

       -f <float> Specify the minimum fraction of mis-matched bases a SNP-containing

              location must have. Its value must between 0 and 1. 0 by default.

       -n <int>
              Specify the minimum number of mis-matched  bases  a  SNP-containing  location  must
              have. 1 by default.

       -r <int>
              Specify the minimum number of mapped reads a SNP-containing location must have (ie.
              the minimum coverage). 1 by default.

       -x <int>
              Specify the maximum number of mapped reads a  SNP-containing  location  have  have.
              3000  by  default. Any location having more than the threshold number of reads will
              not be considered  for  SNP  calling.  This  option  is  useful  for  removing  PCR
              artefacts.

       -s <int>
              Specify  the  minimum base quality scores (Phred scores) read bases must satisfy to
              be used for SNP calling. 13 by default. Read bases with quality scores less than 13
              will be excluded from the analysis.

       -t <int>
              Specify the number of bases trimmed off from each end of the read.  3 by default.

       -T <int>
              Specify the number of threads. 1 by default.

       -v     output version of the program.

       Example:

              exactSNP -i my-alignment.sam -g mm10.fa -o my-SNPs.txt