Version control by dates
BMapBuilder 1.0 (January 2006)
BMapBuilder 2.0 (May 2006)
Major changes in the graphical user interface
BMapBuilder 2.1 (June 2006)
Annotated maps: Instead of SNP positions supplied in the input file, only those SNP positions in a second file (ann1) will be marked in the map in black. A third file (ann2) also containing SNP positions can be supplied and those positions will be marked in the map in red if they are not in the ann1 file and in green if they are.
BMapBuilder 2.2 (April 2008)
Command line interface: For long processes, a non GUI user mode has been added.
BMapBuilder 2.3 (June 2008)
An horizontal coloured bar showing MAF is added in 2D maps on the top of the maps whether MAF is provided with the following meaning:
LD can be compared from two different groups, such as transmitted versus untransmitted haplotypes, female versus male or sample versus individual LD (used to show recombination events when phase is inferred from trios). The difference can be displayed in 2D maps if the input file has a column with values 0, 1 or 2 with the following meaning:
0: Display LD in the chosen color.
1: Display LD in green if chosen color is red or in blue otherwise. As an example, for sample versus undividual LD it would mean LD in this pair is higher assuming non-recombination from the parent in the current file to offspring. Or if comparing Transmitted versus Untransmitted, it would mean one is greater than the other.
2: Display LD in blue if chosen color is red, in red otherwise. It would mean LD in this pair is higher assuming recombination from the parent in the current file to offpspring
BMapBuilder 2.3.2 (February 2009)
BMapBuilder 3.0 (May 2012)
A confidence measure of LD estimation based on the MAF values at each pair of SNPs is used to correct the color map.
As an example, if the default color is green, the color for LD will be cyan (intense cyan, LD=1, white: LD=0) and the color for LD confidence will be yellow (strong confidence (c=1) intense yellow, no confidence at all (c=0) white).
Therefore, in the case LD=1 and c=1 (we are certain about a very high LD), intense yellow with intense cyan will be combined resulting in intense green.
LD=0 and c=1 (we are certain about linkage equilibrium), final color will be intense yellow.
LD=1, c=0 (complete uncertainty about high LD), final color will be intense cyian.
In conclusion, departure of intense green will mean either departure of LD, departure of confidence about the measure of LD or both, so that we should focus in the greenest areas of the LD maps.
Minor changes: Default color has been set up to green.
BMapBuilder 3.1 (March 2013)