Stacks 2.53 populations

The goal of this workflow is to automate all major steps involved with processing common ddRADseq datasets. This is the populations module.

Quick Start

To use Stacks 2.53 import your data in VCF format.
Resources: https://github.com/dportik/Stacks_pipeline/wiki/Stacks-Pipeline-Instructions#RSSA

Test Data

Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> stacks -> test_populations_app

Input File(s)

Use glyma.Wm82.gnm1.div.Z5VC.SNPs.vcf.gz from the directory above as test input.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

Default parameters only, no further configuration needed.

Output File(s)

Expect as output a series of files named after the input file:

glyma.Wm82.gnm1.div.Z5VC.SNPs.p.haplotypes.tsv
glyma.Wm82.gnm1.div.Z5VC.SNPs.p.hapstats.tsv
glyma.Wm82.gnm1.div.Z5VC.SNPs.p.log
glyma.Wm82.gnm1.div.Z5VC.SNPs.p.log.distribs
glyma.Wm82.gnm1.div.Z5VC.SNPs.p.sumstats.tsv
glyma.Wm82.gnm1.div.Z5VC.SNPs.p.sumstats_summary.tsv

Tool Source for App