This ticket is concerning the two bugs in a prototype version (marked v1.4) of Atlas2 that added the always-include (VIP sites) option. Note that this version of Atlas2 was never available through SourceForge, but has been used by some groups. These bugs are not present in any of the versions available through SourceForge. These bugs are specific to Atlas-SNP2. The bugs are detailed below:
The single strand filter, which requires as least one variant read in each strand direction for sites with a read depth of at least 16 did not function. Sites that would have been marked as "strand_filt" were marked as PASS.
When using the "--always-include" option many homozygous reference sample-sites which had data were incorrectly marked as having no data.
These bugs are fixed in the current version of Atlas2.