This release alters how counts and average base qualities are reported in the VCF. Previous versions double counted ambiguous bases and improperly restricted the
BCOUNT field to bases called in the tumor and normal genotypes (see #5). With this release,
DP4 is now more stringent, only counting a read as a reference base if it matches that base exactly.
BCOUNT is similarly more stringent and no longer reports ambiguous bases.
For calculating VAFs from the VCF output, we recommend using the
BCOUNT field's value for your base of interest and dividing by the sum of the values in the
BCOUNT field. This will prevent you from including ambiguous bases in your overall depth measure.
CMAKE_INSTALL_PREFIXis now respected if specified during compilation.
- A compilation error with unit tests on Max OS X (and possibly other platforms) was fixed.
- Numerous documentation updates