Post date: Jun 02, 2017 9:34:42 PM
I downloaded the filtered bcf files for the filtered Medicago truncatula hapmap data. This is the Mt4.0v1 data and can be obtained from here. Here is a README file with inofrmation on the data set. Additional files on gene information, etc. are available from the same site.
There is one bcf file per chromosome (8 chromosomes, plus u = unknown?), chr*-filtered-set-2014Apr15.bcf. These are in /uufs/chpc.utah.edu/common/home/u6000989/projects/mtrunc_mel/mtruncSnps/. Many SNPs contain substantial missing data, so I might want to filter more (plus there are ~60 million SNPs).