Stacks

export_sql.pl

This program provides for the export of all of the Stacks data in a compact form. For each locus, the script reports the consensus sequence, the number of parents and progeny that Stacks could find the locus in, the number of SNPs found at that locus and a listing of the individual SNPs and the observed alleles, followed by the particular allele observed in each individual. The script allows you to specify a number of filters when exporting the data (which are described below).

Program Options

export_sql.pl -D db -b batch_id -a type -f file -o tsv|xls [-m type -c] [-F filter=value ...] [-L lim] [-d] [-h]

Filters

Using the -F flag, multiple filters can be passed to the export_sql.pl program.

Example Usage

~/% export_sql.pl -D tut_radtags -b 1 -f ./stacks/tut_alleles.tsv -o tsv -F snps_l=1 -F snps_u=3

~/% export_sql.pl -D tut_radtags -b 1 -f ./stacks/tut_alleles.xls -o xls -F snps_l=1 -F vprog=130

Other Pipeline Programs

Raw Reads

Core

Execution control

Utilities