Mega2 v4.8.0 released: now reads IMPUTE2 format input

[Dan Weeks]

We have just released a new version of Mega2, version 4.8.0, available from https://watson.hgen.pitt.edu/register  

The main new feature is that Mega2 now can read as input imputed genotype data in IMPUTE2 format.  

The new version reads VCF format input files more quickly than before.

Enhancements in Mega2 version 4.8.0

• Mega2 now supports reading imputed data in IMPUTE2 (Oxford) format (genotype/sample).
• Several issues affecting the performance processing VCF files have been fixed. Reading in VCF format data is now much faster than it was previously.
• The Mega2 log file now contains essentially what is displayed on the screen during program execution. The voluminous, complete listing of errors and warnings is now only in the Mega2 ERR(or) log file.
• Bug: PLINK Binary file generation in “individual major” order had been wrong and is now fixed. Note: the common SNP major order did not have this problem.
• Bug: S.A.G.E. Analysis and Mega2 Analysis modes did not correctly carry through non-numeric alleles to their output files.