The GangSTR is a tool for genome-wide profiling tandem repeats from short reads, it can handle repeats that are longer than the read length.

References:

• Mousavi N, Shleizer-Burko S, Yanicky R, Gymrek M. Profiling the genome-wide landscape of tandem repeat expansions.Nucleic Acids Res. 2019 Sep 5;47(15):e90. doi: 10.1093/nar/gkz501.PubMed |  Journal

• GangSTR Github:Github

• Module Name: GangSTR (see the modules page for more information)
• Current GangSTR command lines could be run as:

  	GangSTR
  	

  Interactive job
  Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

  Allocate an interactive session and run the program.
  Sample session (user input in bold):

  [user@biowulf]$ sinteractive
  salloc.exe: Pending job allocation 46116226
  salloc.exe: job 46116226 queued and waiting for resources
  salloc.exe: job 46116226 has been allocated resources
  salloc.exe: Granted job allocation 46116226
  salloc.exe: Waiting for resource configuration
  salloc.exe: Nodes cn3144 are ready for job
  
  [user@cn3144 ~]$ module load GangSTR
  [user@cn3144 ~]$ mkdir /data/$USER/GangSTR_test/
  [user@cn3144 ~]$ cd /data/$USER/GangSTR_test/
  [user@cn3144 ~]$ cp $GANGSTR_TEST_DATA/* .
  [user@cn3144 ~]$ GangSTR --help
  Usage: GangSTR [OPTIONS] --bam  --ref  --regions  --out 
  
   Required options:
  	--bam         	Comma separated list of input BAM files
  	--ref              	FASTA file for the reference genome
  	--regions        	BED file containing TR coordinates
  	--out              	Prefix to name output files
  
   Additional general options:
  	--targeted                    	Targeted mode
  	--chrom                       	Only genotype regions on this chromosome
  	--bam-samps           	Comma separated list of sample IDs for --bam
  	--samp-sex            	Comma separated list of sample sex for each sample ID (--bam-samps must be provided)
  	--str-info            	Tab file with additional per-STR info (see docs)
  	--period              	Only genotype loci with periods (motif lengths) in this comma-separated list.
  	--skip-qscore                 	Skip calculation of Q-score
  
   Options for different sequencing settings
  	--readlength             	Read length. Default: -1
  	--coverage             	Average coverage. must be set for exome/targeted data. Comma separated list to specify for each BAM
  	--model-gc-coverage           	Model coverage as a function of GC content. Requires genome-wide data
  	--insertmean           	Fragment length mean. Comma separated list to specify for each BAM separately.
  	--insertsdev           	Fragment length standard deviation. Comma separated list to specify for each BAM separately.
  	--nonuniform                  	Indicate whether data has non-uniform coverage (i.e., exome)
  	--min-sample-reads       	Minimum number of reads per sample.
  
   Advanced paramters for likelihood model:
  	--frrweight            	Weight for FRR reads. Default: 1
  	--enclweight           	Weight for enclosing reads. Default: 1
  	--spanweight           	Weight for spanning reads. Default: 1
  	--flankweight          	Weight for flanking reads. Default: 1
  	--ploidy                 	Indicate whether data is haploid (1) or diploid (2). Default: -1
  	--skipofftarget               	Skip off target regions included in the BED file.
  	--read-prob-mode              	Use only read probability (ignore class probability)
  	--numbstrap              	Number of bootstrap samples. Default: 100
  	--grid-threshold         	Use optimization rather than grid search to find MLE if more than this many possible alleles. Default: 10000
  	--rescue-count           	Number of regions that GangSTR attempts to rescue mates from (excluding off-target regions) Default: 0
  	--max-proc-read          	Maximum number of processed reads per sample before a region is skipped. Default: 3000
  
   Parameters for local realignment:
  	--minscore               	Minimum alignment score (out of 100). Default: 75
  	--minmatch               	Minimum number of matching basepairs on each end of enclosing reads. Default: 5
  
   Default stutter model parameters:
  	--stutterup            	Stutter insertion probability. Default: 0.05
  	--stutterdown          	Stutter deletion probability. Default: 0.05
  	--stutterprob          	Stutter step size parameter. Default: 0.9
  
   Parameters for more detailed info about each locus:
  	--output-bootstraps           	Output file with bootstrap samples
  	--output-readinfo             	Output read class info (for debugging)
  	--include-ggl                 	Output GGL (special GL field) in VCF
  
   Additional optional paramters:
  	-h,--help                     	display this help screen
  	--seed                        	Random number generator initial seed
  	-v,--verbose                  	Print out useful progress messages
  	--very                        	Print out more detailed progress messages for debugging
  	--quiet                       	Don't print anything
  	--version                     	Print out the version of this software.
  
  
  This program takes in aligned reads in BAM format
  and outputs estimated genotypes at each TR in VCF format.
  
  [user@cn3144 ~]$  GangSTR --bam nc10_25.sorted.bam --ref \
  /fdb/igenomes/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa --regions HTT.bed --out GangSTR_out
  [GangSTR-2.5.0] ProgressMeter: Loading read group id CompMultiLoc_1_cov50_readLen_100 for sample 10_25
  [GangSTR-2.5.0] ProgressMeter: Processing chr4:3074877
  [GangSTR-2.5.0] ProgressMeter: 	Genotyper Results:  10, 25	likelihood = 1275.52
  [user@cn3144 ~]$ exit
  salloc.exe: Relinquishing job allocation 46116226
  [user@biowulf ~]$
  

  Batch job
  Most jobs should be run as batch jobs.

  Create a batch input file (e.g. GangSTR.sh). For example:

  
  #!/bin/bash
  set -e
  module load GangSTR
  GangSTR \
    --bam nc10_25.sorted.bam \
    --ref /fdb/igenomes/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa \
    --regions HTT.bed \
    --out GangSTR_out
  
  

  Submit this job using the Slurm sbatch command.

  sbatch --cpus-per-task=2 --mem=2g GangSTR.sh

  Swarm of Jobs
  A swarm of jobs is an easy way to submit a set of independent commands requiring identical resources.

  Create a swarmfile (e.g. GangSTR.swarm). For example:

  
  cd dir1;GangSTR --bam test1.bam --ref genome.fa --regions test1.bed --out test1 
  cd dir1;GangSTR --bam test2.bam --ref genome.fa --regions test2.bed --out test2 
  

  Submit this job using the swarm command.

  swarm -f GangSTR.swarm [-t #] [-g #] --module GangSTR

  where

  -g #	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
  -t #	Number of threads/CPUs required for each process (1 line in the swarm command file).
  --module GangSTR	Loads the GangSTR module for each subjob in the swarm