Hi All,

We have a new Atlas2 stable release version 1.4.3 . Please either use the link below to download the latest version or the code can also be checked out of sourceforge subversion.


Moving forward we will be utilising the mailing list functionality within sourceforge to send out notifications. Please sign up to get updates on releases and major bug fixes. We would also very much appreciate if bug reports and feature requests came through the sourceforge ticketing system.

Mailing List:


Here is what's been added / changed in the latest version.

1.Add an option “-w” to only evaluate the sites in a given VIP list.
2.Atlas-SNP2 will evaluate the VIP sites of extra-high coverage, regardless of the setting of “maximum coverage”. And these VIP sites will be marked as “high_coverage” in the filter column if they are higher than “maximum coverage”. (In previous version, these sites are skipped)
3.Require the users to set the sequencing platform. The labels are “--Illumina” ,”454_FLX”,”454_XLR”. To make it compatible to previous submission scripts of various users, “-s” for Illumina data will still work.
1. Bug fixed in -always-include option which caused included low-Quality sites to be printed with a QUAL of 'false' and missing the P value. 
2. Removed the ReqIncl filter, this is now only indicated in the INFO column.
1. New "--fast" implemented. Since it uses memory for storing variant information across all samples should only be used to merge small number of sites (~50000) across small number of samples (~20).
2. New option "--cluster". Designed to be used in a HPC environment. Useful when merging millions of variants across thousands of samples.
3. Logging implemented. 
Please refer to sourceforge wiki for more detailed information.

Atlas2 Team.