FDSTools

FDSTools (Forensic DNA Sequencing Tools) is a collection of tools for analysing massively parallel sequencing data of forensic DNA markers such as STRs and SNPs. It characterises and filters PCR stutter and other systematic noise, and detects the true alleles in a sample. Alleles are named with the STRNaming nomenclature.

FDSTools

License

Free to use and open source under GNU GPLv3.

Available

Roihu-CPU: 2.2.1 (module py-fdstools), via the bio-apps module.

Usage

FDSTools is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the FDSTools module:

module load bio-apps/v202603
module load py-fdstools/2.2.1

All tools are run through the fdstools command. List the tools, or show the options of a single tool, with:

fdstools --help
fdstools --help tssv

Analysis pipelines

The pipeline tool runs complete, predefined analyses configured with an INI file. There are three analysis types:

reference-sample: runs a single reference sample through TSSV and Stuttermark.
reference-database: builds a database of systematic noise from a collection of reference samples.
case-sample: runs a single case sample through TSSV, BGPredict, BGMerge, BGCorrect and Samplestats.

The analyses need a library file that describes your markers. Create one with fdstools library mylibrary.txt and fill in your markers.

If the INI file does not exist yet, pipeline creates it with the default settings for the chosen analysis type:

fdstools pipeline case.ini --analysis case-sample

Fill in the input files and settings in case.ini, then run the analysis:

fdstools pipeline case.ini

Read counting with TSSV is the slowest step. To use several cores, set num-threads in the [tssv] section of the INI file to the number of cores reserved for the job.

Running individual tools

The tools can also be run one at a time. For tools that process sample data files, such as stuttermark, bgcorrect, samplestats and seqconvert, give the input files with -i and the output files with -o:

fdstools samplestats -i sample.csv -o sample_stats.csv

You can also give the input and output files as plain arguments (fdstools samplestats sample.csv sample_stats.csv). For tools that take another argument first, such as the format in seqconvert, put the files directly after it, with no options in between:

fdstools seqconvert allelename sample.csv sample_named.csv -l mylibrary.txt

Example batch script

#!/bin/bash
#SBATCH --job-name=fdstools
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=02:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load py-fdstools/2.2.1

fdstools pipeline case.ini

With num-threads = 4 in the [tssv] section of case.ini, TSSV uses all four cores reserved for the job. Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk