NAME

       exactSNP - toolkit for processing next-gen sequencing data

DESCRIPTION

       Version 2.0.4

       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 Alexandre Mestiashvili for the Debian distribution and
        can be used for any other usage of the program.

exactSNP 2.0.3                                     March 2023                                        EXACTSNP(1)