STRipy-pipeline is non-graphical command-line version of STRipy that can be integrated into pipelines and analyse multiple STR or VNTR loci in parallel.

References:

• Halman, A., Dolzhenko, E. & Oshlack, A.
  STRipy: A graphical application for enhanced genotyping of pathogenic short tandem repeats in sequencing data Human Mutation, 43(7), 859-868. 2022
  DOI: https://doi.org/10.1002/humu.24382
  

• STRipy-pipeline Gitlab

• Module Name: stripy-pipeline (see the modules page for more information)
• Unusual environment variables set
  • STRIPY_PIPELINE_HOME  executable directory

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive 
[user@cn4471 ~]$ module load stripy-pipeline
[+] Loading stripy-pipeline  2.5  on cn4284
[+] Loading singularity  4.0.1  on cn4284
[+] Loading samtools 1.19  ...
[+] Loading REViewer  0.2.7
[+] Loading expansionhunter  5.0.0  on cn4284

[user@cn4471 ~]$ cp -a $STRIPY_PIPELINE_HOME/examples .
[user@cn4471 ~]$ python3 $STRIPY_PIPELINE_HOME/stri.py -h
usage: stri.py [-h] --input INPUT [--locus LOCUS] [--custom CUSTOM] [--sex {male,female}] [--genome {hs1,hg38,hg19}] --reference REFERENCE [--analysis {standard,extended}]
               [--output OUTPUT] [--logflags LOGFLAGS] [--config CONFIG]

optional arguments:
  -h, --help            show this help message and exit
  --input INPUT         Input file (indexed BAM or CRAM)
  --locus LOCUS         Loci to genotype
  --custom CUSTOM       Custom loci file path (BED file)
  --sex {male,female}   Sex of the sample
  --genome {hs1,hg38,hg19}
                        Name of the reference genome
  --reference REFERENCE
                        Reference genome (FASTA file)
  --analysis {standard,extended}
                        Analysis type
  --output OUTPUT       Output folder
  --logflags LOGFLAGS   File path of the output log file
  --config CONFIG       File path of the config file

[user@cn4471 ~]$ python3 $STRIPY_PIPELINE_HOME/stri.py \
      --genome hg38 \
      --reference /fdb/genomebrowser/fasta/hg38/hg38.fa \
      --output results/ \
      --locus AFF2,ATXN3,HTT,PHOX2B \
      --input examples/Sample001_hg38.bam
Starting analysis (examples/Sample001_hg38.bam)
Analysis finished (examples/Sample001_hg38.bam)

[user@cn4471 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$