exactSNP - a SNP caller that discovers SNPs by testing signals
against local background noises
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.
Example:
- exactSNP -i my-alignment.sam -g mm10.fa -o
my-SNPs.txt