AgileSamFileMerger reads the sequence entries in two or more ordered *.sam files and combines all the entries in the original files into a single *.sam file.
AgileGenotyper will create a pseudo-microarray SNP genotyping file from an ordered SAM file containing exon sequence data. The file will contain the genotype data at over 0.5 million SNP sites previously identified by the 1000 Genomes project. Such a file can then be used as a data source for a mapping program designed for analyzing Affymetrix microarray SNP data.