Disperse can include SNP data into the target files that are processed by PieceMaker. This allows PieceMaker to discard restriction fragments that have undefined ends due to known nucleotide variation in a restriction site.
It also allows fragments to be discarded if there are SNPs located in the regions to which a selector probe would hybridize. Both these conditions could introduce unwanted bias into the amplification, and are probably best avoided.
Using SNP data with disperse requires downloading a SNP data file, and placing it into the correct location, or editing the config file to reflect the location. See see Download and Installation and configuration for details.
If not using the SNP data file, use the -nosnp option on the command line, or alternatively, create an empty text file in the SNP data file location specified in your configuration.
To use your own set of variations, create your own data file using the following format:
919643 NC_000010.9 347848 347850 T/C 947469 NC_000010.9 522161 522163 T/C
where the fields are tab-delimited and with the following meaning:
1. ID of the variation
2. Accession number of the sequence the variation is on (NCBI chromosome assemblies)
3. Coordinate (1-based) of the last base 5' of the variation that is unaffected by the variation
4. Coordinate (1-based) of the first base 3' of the variation that is unaffected by the variation
5. Possible variants, separated by '/', that occur in the position.
Note that only single-nucleotide substitutions will be considered by the software, even if other types of variations are permitted in the variation master file.