lobSTR: a short tandem repeat profiler for next generation sequencing data

genotyping y-str/codis
validation sets

lobSTR compiled binaries

lobSTR source code

lobSTR call sets

Below are links to VCFs we've generated using lobSTR for a variety of population-scale sequencing projects.

lobSTR source code on Github

The lobSTR source code is available on github. To get the latest version, you can pull the code from the current git repo:

git clone https://github.com/mgymrek/lobstr-code.git lobstr-code

Then follow the installation instructions for building from source.

Contact mgymrek AT mit DOT edu if you are interested in being involved with lobSTR development.

lobSTR v3.+ index

Starting with lobSTR v3.0.0+, we have changed our index structure. This index is not compatible with previous lobSTR versions.

lobSTR v2. index

Contains loci for periods 1 through 6 as well as markers obtained from CODIS, Marshfield and Y-STR datasets. Resource bundles contain a table of STR loci, the lobSTR index, and the file needed for the --strinfo option for the allelotyping step.

Allelotype validation suite resources (for developers)

Contains resources for comparing Marshfield markers between lobSTR and capillary electrophoresis data using the allelotype_validation_suite.sh script. Email the user group for more details or if you're interested in contributing to lobSTR!

Previous versions

To see a list of changes and download previous lobSTR code and index versions, see the changelog page.