Stacks

markers.pl

This script examines loci in the catalog and defines mappable alleles. Loci are coded according to the configuration of alleles at that locus in the catalog. For example, a locus encoded as ab/aa implies that there are two alleles at this locus (a and b), and the male parent is heterozygous at that locus (ab) while the female parent is homozygous (aa). Progeny matched against this locus in the catalog must have some combination of the a and b alleles (aa and ab would be viable allele combinations in the progeny, while bb would be impossible) and the program will tally of how many of each allele is present in the population. These data are made available through the web interface.

After execution, the output file should be loaded into the markers table of Stacks database. The denovo_map.pl program will execute the markers.pl script and load the resulting data automatically.

Program Options

markers.pl -b id [-D db] [-o path] [-d] [-h]

Mappable Marker Types

Stacks understands several different marker types, available from different types of mapping crosses. Stacks orders the markers according to which parent was loaded into the database first. In the marker definitions below, we assume the male parent of the cross was loaded prior to the female (and hence would have a lower Sample ID).

Example Usage

~/% markers.pl -D tut_radtags -b 1 -o ./stacks/