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


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

-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

-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.


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

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