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. 1000  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

exactSNP 1.6.0+dfsg                               November 2017                                      EXACTSNP(1)