GangSTR is a tool for genome-wide profiling tandem repeats from short reads. A key advantage of GangSTR over existing tools (e.g. lobSTR or hipSTR) is that it can handle repeats that are longer than the read length.
GangSTR takes aligned reads (BAM) and a set of repeats in the reference genome as input and outputs a VCF file containing genotypes for each locus.
bioRxiv preprint manuscript: http://bit.ly/gangstr-preprint
For questions on installation or usage, please open an issue, submit a pull request, or contact Nima Mousavi (mousavi@ucsd.edu).
Download | Install | Usage | File formats | References
The latest GangSTR release is available on the releases page.
For a list of TR references available, see references below.
GangSTR requires third party packages nlopt, gsl, and htslib.
If you are installing from the tarball (which for most purposes you should be), the following instructions will install all dependencies as well as GangSTR itself. Both UNIX and Mac OSX are supported.
If you are attempting to compile and install directly from a cloned github repository (e.g. if you would like the latest and greatest unreleased feature or would like to contribute a fix or new feature), the following steps will not work and you should follow instructions under "Compiling from git source" below.
It has been tested and verfied against the following gcc compiler versions: 4.9.2, 5.4.0, 6.3.0, 7.3.0
If you are running as root:
tar -xzvf GangSTR-X.X.tar.gz
cd GangSTR-X.X
sudo ./install-gangstr.sh
If you are installing locally (e.g. on a cluster where you don't have root access):
tar -xzvf GangSTR-X.X.tar.gz
cd GangSTR-X.X
./install-gangstr.sh PREFIX
where PREFIX is a place you have write permissions. In most cases this will be your home directory, e.g. $HOME. If you install locally, make sure $PREFIX/bin is on your PATH.
Typing GangSTR --help should show a help message if GangSTR was successfully installed.
To compile from git source, first make sure nlopt, gsl, and htslib are installed, then run the following:
# Clone the repo
git clone https://github.com/gymreklab/GangSTR
cd GangSTR/
# Generate the configure script
./reconf
# Compile and install GangSTR
./configure
make
make install
To run GangSTR using default parameters use the following command:
GangSTR --bam file.bam
--ref ref.fa
--regions regions.bed
--out outprefix
Required parameters:
- --bam Alignment file (.bam)
- --ref Refererence genome (.fa)
- --regions Target TR loci (.bed)
- --out Output prefix
Additional general options:
- --genomewide Run GangSTR in genome-wide mode. This mode has more stringent filtering steps to prevent false positive in genome-wide profiling.
Options for different sequencing settings
- --readlength <int> Preset read length (default: extract from alignments if not provided)
- --coverage <float> Preset average coverage, should be set for targeted data (default: calculate if not provided)
- --nonuniform Indicates non-uniform coverage in alignment file (i.e., used for exome sequencing). Using this flag removes the likelihood term corresponding to FRR count.
Advanced parameters for likelihood model:
- --frrweight <float> Reset weight for FRR class in likelihood model (default 0.5)
- --spanweight <float> Reset weight for Spanning class in likelihood model (default 1.0)
- --enclweight <float> Reset weight for Enclosing class in likelihood model (default 1.0)
- --flankweight <float> Reset weight for Flanking class in likelihood model (default 1.0)
- --ploidy [1,2] Haploid (1) or diploid (2) genotyping (default 2)
- --useofftarget Extract off-target FRRs based on the off-target regions provided in the regions file.
- --insertmean <float> Fragment length mean (default: calculate if not provided)
- --insertsdev <float> Fragment length standard deviation (default: calculate if not provided)
- --insertmax <float> Maximum allowed fragment length (default: no filtering based on fragment length)
- --readprobmode Only use read probabilities in likelihood model (ignore class probability)
- --numbstrap <int> Number of bootstrap samples for calculating confidence intervals (default 100)
Parameters for local realignment:
- --minscore <int> Minimun alignment score for accepting reads (default 75)
- --minmatch <int> Minimum matching basepairs required at the edge of the repeat region to accept flanking and enclosing reads (default 5)
Stutter model parameters:
- --stutterup <float> Stutter insertion probability (default 0.0364653)
- --stutterdown <float> Stutter deletion probability (default: 0.0428387)
- --stutterprob <float> Stutter step size parameter (default: 0.818913)
Parameters for more detailed info about each locus:
- --output-readinfo Output a file containing extracted read information
- --output-bootstraps Output a file containing bootstrap samples
Additional optional parameters:
- -h,--help display help screen
- --seed Random number generator initial seed
- -v,--verbose Print progress information (major steps)
- --very Print detailed progress information
- --version Print out the version of this software
GangSTR takes as input a BAM file of short read alignments, a reference set of TRs, and a reference genome, and outputs genotypes in a VCF file. Each of these formats is described below.
GangSTR requires a BAM file produced by an indel-sensitive aligner. The BAM file must be sorted and indexed e.g. by using samtools sort and samtools index. GangSTR currently only processes a single sample at a time.
You must input a reference genome in FASTA format. This must be the same reference build used to align the sequences in the BAM file.
GangSTR requires a reference set of regions to genotype. This is a BED-like file with the following columns:
- The name of the chromosome on which the STR is located
- The start position of the STR on its chromosome
- The end position of the STR on its chromosome
- The motif length
- The repeat motif
An optional 6th column may contain a comma-separated list of off-target regions for each TR. These are regions where misaligned reads for a given TR may be incorrectly mapped.
Below is an example file which contains 5 TR loci. Standard references for hg19 and GRCh38 can be obtained below. NOTE: The table header is for descriptive purposes. The BED file should not have a header
| CHROM | START | END | MOTIF_LEN | MOTIF | OFFTARGET (optional) |
|---|---|---|---|---|---|
| chr1 | 10689 | 10700 | 5 | CGCGC | |
| chr1 | 28589 | 28603 | 1 | T | |
| chr4 | 11173 | 11194 | 11 | CGCCGGCGCGG | |
| chr4 | 150889 | 150909 | 2 | TG | |
| chr19 | 45770205 | 45770264 | 3 | CAG | chr2:163338502-163338506,chr3:197333949-197333955,chr6:16327632-16327646,chr6:170561926-170561931,chr7:122288209-122288215,chr8:133055822-133055827,chr11:28310883-28310888,chr17:4887671-4887677,chr18:55586148-55586165,chr19:13207866-13207871 |
For more information on VCF file format, see the VCF spec. In addition to standard VCF fields, GangSTR adds custom fields described below.
INFO fields contain aggregated statistics about each TR. The following custom fields are added:
| FIELD | DESCRIPTION |
|---|---|
| END | End position of the TR |
| RU | Repeat motif |
| REF | Reference copy number (number of repeat units |
FORMAT fields contain information specific to each genotype call. The following custom fields are added:
| FIELD | DESCRIPTION |
|---|---|
| GB | Base pair length differences of genotype from reference for each allele |
| CI | 95% confidence intervals for each allele |
| RC | Number of reads in each class (enclosing, spanning, FRR, flanking) |
| Q | Minimum negative likelihood |
| INS | Insert size mean and stddev at the locus |
The following lists available references created using Tandem Repeats Finder. We update the reference periodically with additional loci or annotation changes. Please see the Changelog file for details. Note references must be unzipped before using with GangSTR.
| Reference build | Version | Link | Comment |
|---|---|---|---|
| hg19 | ver8 | hg19_ver8.bed.gz | Motifs of up to 15 bps |
| hg19 | ver10 | hg19_ver10.sorted.bed.gz | Motifs of up to 20 bps, includes ChrX and ChrY |
| hs37 | ver8 | hs37_ver8.bed.gz | Motifs of up to 15 bps |
| hg38 | ver5 | hg38_ver5.bed.gz | Motifs of up to 15 bps |
| hg38 | ver6 | hg38_ver6.sorted.bed.gz | Motifs of up to 20 bps, includes ChrX and ChrY |
The references below contain pre-defined off-target loci for target pathogenic loci (hg38 coordinates):
| Locus | hg38 Link | hg19 Link |
|---|---|---|
| SCA1 | SCA1_hg38.bed | SCA1_hg19.bed |
| SCA2 | SCA2_hg38.bed | SCA2_hg19.bed |
| SCA3 | SCA3_hg38.bed | SCA3_hg19.bed |
| SCA6 | SCA6_hg38.bed | SCA6_hg19.bed |
| SCA7 | SCA7_hg38.bed | SCA7_hg19.bed |
| SCA8 | SCA8_hg38.bed | SCA8_hg19.bed |
| SCA12 | SCA12_hg38.bed | SCA12_hg19.bed |
| SCA17 | SCA17_hg38.bed | SCA17_hg19.bed |
| HTT | HTT_hg38.bed | HTT_hg19.bed |
| DM1 | DM1_hg38.bed | DM1_hg19.bed |
| FMR1 | FMR1_hg38.bed | FMR1_hg19.bed |