exactSNP - a SNP caller that discovers SNPs by testing signals against local
exactSNP [options] -i
- -i <file>
- Specify name of an input file including read mapping
- [-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.
- -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.
- Indicate the input file provided via -i is in BAM
- -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
<float> Specify the minimum fraction of mis-matched bases a
- location must have. Its value must between 0 and 1. 0 by
- -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.
- output version of the program.
- exactSNP -i my-alignment.sam -g mm10.fa