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.Atlas2-INDEL
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.VcfPrinter
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.