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