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.


Important Notes

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@biowulf]$ sinteractive 
[user@cn4471 ~]$ module load stripy-pipeline
[+] Loading stripy-pipeline  1.2  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
Copy sample data to the current folder:
[user@cn4471 ~]$ cp -a $STRIPY_PIPELINE_HOME/examples .
[user@cn4471 ~]$ python3 $STRIPY_PIPELINE_HOME/
usage: [-h] --input INPUT [--locus LOCUS] [--custom CUSTOM]
               [--sex {male,female}] [--genome {hs1,hg38,hg19}] --reference
               REFERENCE [--analysis {standard,extended}] [--output OUTPUT]
               [--logflags LOGFLAGS] [--config CONFIG] error: the following arguments are required: --input, --reference
Running STRipy on single sample:
[user@cn4471 ~]$ python3 $STRIPY_PIPELINE_HOME/ \
      --genome hg38 \
      --reference /fdb/genomebrowser/fasta/hg38/hg38.fa \
      --output results/ \
      --locus AFF2,ATXN3,HTT,PHOX2B \
      --input examples/Sample001_hg38.bam
Starting analysis (examples/Sample001_hg38.bam)
Analysis finished (examples/Sample001_hg38.bam)
[user@cn4471 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$