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fastStructure

fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. fastStructure Homepage

Available Modules

module load fastStructure/1.0-gimkl-2020a-Python-2.7.18

Using fastStructure executables

While the modules are python scripts, they must be run as executables, not python scripts, as in the following sbatch.

#!/bin/bash -e

#SBATCH --job-name        fastStructure
#SBATCH --account         nesi12345
#SBATCH --time            01:00:00
#SBATCH --mem             2G

module purge
module load fastStructure/1.0-gimkl-2020a-Python-2.7.18

structure.py -K 3 --input=<infile> --output=<outfile>

The distruct.py module may cause issues due to the module wanting to open a new window to view the plot. You may be able to work around this by telling matplotlib to write the plot to a file:

env MPLBACKEND='svg'
distruct.py --output myplot.svg

Thanks to our friends at Purdue for their documentation about these issues.

fastStructure .str format

fastStructure can take inputs in the form of a .bed file or an .str format Despite using the same .str suffix, the format required for fastStructure differs from that required for Structure. For fastStructure, no header row is required, but the first 6 columns of the file are ignored and there must be two lines per sample. Below is an example input (input.str) that will work with fastStructure:

#   #   #   #   Smpl_ID Pop_ID  Locus_1 Locus_2 Locus_3 Locus_4 Locus_5 Locus_6 Locus_7 Locus_8 Locus_9 Locus_10
#   #   #   #   Sample1 1   1   -9  0   1   0   1   1   1   1   0
#   #   #   #   Sample1 1   1   -9  1   0   1   0   0   0   0   1
#   #   #   #   Sample2 2   0   0   1   1   1   0   1   1   0   1
#   #   #   #   Sample2 2   1   0   1   0   1   1   0   1   0   1

To use this, use the --format=str flag and include the file without the file extension --input=input or fastStructure will append an extra .str to the filename.

Shout out to a rather old blog post for solving this issue!

The .str files output by ipyrad should work without issue. Otherwise you may want to convert .vcf files to .bed files using another tool and proceed with fastStructure using the .bed files.