NAME

       exactSNP - toolkit for processing next-gen sequencing data

DESCRIPTION

       Version 2.0.1

       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 (gzipped file is accepted).  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  depth a SNP location is allowed to have.  1,000,000 reads by
              default. 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.

       -C <path>
              Specify the path to save the temporary files.

       Example:

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

AUTHOR

        This manpage was written by Nilesh Patra for the Debian distribution and
        can be used for any other usage of the program.