We used Picard v.1.57 [ http://picard.sourceforge.net/] to merge mapping files for each individual from different SOLiD runs and adjust read group headers.
Many of the problems are a result of merging map data, some of it flawed, from many sources.
The ICuGI (International Cucurbit Genomics Initiative) merged map is available in the Cucurbit Genomics Database (http://www.icugi.org).
Bold markers are anchor markers in the consensus map (Diaz et al. 2011) or common markers on the ICuGI merged map from the Cucurbit Genomics Database (http://www.icugi.org).
That was the thinking at O'Reilly Media Where 2.0, a conference where hundreds gathered this week to celebrate a concept that barely existed a year ago: the "mash-up," which merges map data from the likes of Google and Microsoft with…well, pretty much anything.
Each merged map was plotted along with all its component maps on a plot of marker number against genetic map distance.
Nonetheless, model ensemble methods proved to be useful for merging maps with different types of datasets, spatial coverage, and methodological approaches.
blockbuster merges mapped reads into blocks based on their location in the reference genome.
They also designed an algorithm for merging maps from different studies on the basis of loci common to different maps.
We used LPmerge (Endelman and Plomion 2014) to generate a composite map from the 10 component maps we had generated because it merges maps without recalculating recombination frequencies, drastically reducing the computational time required.
