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HipSTR

HipSTR can be used to obtain STR (Short tandem repeat) genotypes. The bundle packages version 0.7.

Usage example

Load the module using the following command:

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module load hipstr

The module makes the following commands available:

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filter_haploid_vcf.py
filter_vcf.py
generate_aln_html.py
GetStutterModels
HipSTR
html_alns_to_pdf.py
VizAln
VizAlnPdf

The hipstr_shell command can be used to access a shell in the bundle.

Run pet list -t hipstr for a list of examples.

Performance notes

No performance notes available

HipSTR should be run on a system with at least 8 GB of RAM and 1 thread.

Benchmarks

No benchmarks available.

Community guides and tutorials

  • No community guides available.

Official site and documentation

Licensing information

HipSTR is licensed under the GNU GPL v2.0.

Primary citation

Willems, T., Zielinski, D., Yuan, J. et al. Genome-wide profiling of heritable and de novo STR variations. Nat Methods 14, 590–592 (2017). doi

External guides and resources

  • If you know of a guide/tutorial that you have found useful, please help us share it by contacting the HPC staff at hpc@ufs.ac.za