• Migration of the vcftools project (and website) from sourceforge to github
• Optimizations for reading and writing BCF files
• Edits to code for C++ 11 compatibility
• Added --mendel option for finding Mendelian errors in trios
• Allow --diff options to output to stream by splitting up function into --diff-site and --diff-indv options
• Added experimental --hapcount function to determine the amount of unique haplotypes in user defined bins
• Addition of "any" options to filter by frequency or count of any alternate allele (instead of requiring all of them to pass)
• Improvements to temporary file handling for all LD functions
• Added --chrom-map option to allow user specified chromosomes for writing out plink files
• Allow site filtering with multiple keep and exclude files
• Tajima's D now reports NaN in the absence of data
• Various bug fixes