ProbABEL v0.2.2 release

We are happy to announce a new release of ProbABEL: version 0.2.2 is out!
This version is an incremental update of v0.2.0, featuring several bug fixes and some new functionality in the script.

New functionality:

  • Update of the script and probabel_config.cfg. The .cfg file now accepts the chr separator in multiple locations in the path (thanks to Marijn Verkerk). can now also run Y chromosome analysis and the help message has been updated.
  • and probabel_config.cfg now also accept chunks, where dose, prob, info and map files are split into multiple chunks. This is now the default for people following the 1000 genomes imputation cookbook for MaCH/minimac (the recipe uses the chunkchromosome tool to split the data into smaller pieces, speeding up imputation on computer clusters). See probabel_config.cfg.example for an example.

Bugs fixed in this release:

  • Fixed bug #2295: the inverse variance-covariance matrix (used with the --mmscore option) was incorrectly subsetted when NAs are present for one or more SNP dosages (so this is not an issue for people using imputed data). As a result the invvarmatrix that was actually used in the regression contained rows and columns of zeroes. Thanks to Maarten Kooyman for reporting this bug.
  • Fixed bug #1186: When .map file is missing (but --map option was given), the wrong error message was displayed. Thanks to Nicola Pirastu for reporting this bug.
  • Fixed bug #2147: The value of the Rsq column in the info file should be > 0, unlike what was mentioned in the documentation.

Were to get it:

  • The source package can be found on the GenABEL website at:
  • Users of Ubuntu (or one of its derivative distributions like Kubuntu or Linux Mint) can install the latest ProbABEL release from the GenABEL PPA (Personal Package Archive) by following these steps:
    sudo add-apt-repository ppa:l.c.karssen/genabel-ppa
    sudo apt-get update
    sudo apt-get install probabel

For user support, please take a look at our forums at Bugs can be reported in our bug tracker on r-forge.

This release was partially sponsored by the Erasmus Medical Centre in Rotterdam, NL.