Several issues have been observed with the recent 1.8.0 release of APT. Specifically:
The txt output (--txt-output option) from apt-probeset-genotype will report forced calls when doing a birdseed analysis, as opposed to applying a confidence-score cutoff to produce no-calls for uncertain genotypes. A future release of APT will phase out the --txt-output option. It is recomended that you use the table text output (--table-output) or AGCC CHP file output (--cc-chp-output). Note that the table output is enabled by default.
When using the force option (--force) with apt-probeset-genotype, the ?Chip Type? field in the resulting CHP files will be empty. The result is CHP files which most applications will be unable to load, including Genotyping Console. A future release of APT will report the CDF Chip Type in the CHP file output.
The current implementation of birdseed will generate incorrect answers on Solaris-Sparc. Because of this, no Solaris-Sparc binaries were provided. Users compiling APT from source code on Solaris-Sparc machines should note that they should not use their binaries to generate birdseed results.
We anticipate correcting these in the next APT release.
