What it does
This program expects data that have been aligned to a reference genome, and can accept data directly from Bowtie, or from any aligner that can produce SAM format. To avoid datasets names problems, we recommand the use of the Map with BWA for STACKS tool. This program will execute each of the Stacks components: first, running pstacks on each of the samples specified, building loci (based on the reference alignment) and calling SNPs in each. Second, cstacks will be run to create a catalog of all loci specified as 'parents' or 'samples' on the command line, again using alignment to match loci in the catalog. Finally, sstacks will be executed to match each sample against the catalog. The ref_map.pl program will also load the results of each stage of the analysis: individual loci, the catalog, and matches against the catalog into the database (although this can be disabled). After matching the program will build a database index to speed up access (index_radtags.pl) and enable web-based filtering.
Input files
SAM, BAM
Population map:
indv_01 1 indv_02 1 indv_03 1 indv_04 2 indv_05 2 indv_06 2
Output files
Notes: For the tags file, each stack will start in the file with a consensus sequence for the entire stack followed by the flags for that stack. Then, each individual read that was merged into that stack will follow. The next stack will start with another consensus sequence.
Notes: If a stack has two SNPs called within it, then there will be two lines in this file listing each one.
Notes: Each line in this file records a match between a catalog locus and a locus in an individual, for a particular haplotype. The Batch ID plus the Catalog ID together represent a unique locus in the entire population, while the Sample ID and the Stack ID together represent a unique locus in an individual sample.
Created by:
Stacks was developed by Julian Catchen with contributions from Angel Amores, Paul Hohenlohe, and Bill Cresko
Project links: