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Combining two or more sorted SAM files into one sorted SAM file

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. The sequence reads in the merged *.sam file are all sorted by chromosome and chromosomal position. Reads not mapped to the reference sequence are discarded. However, if a sequence is a duplicate of another read it will be retained.

AgileSamFileMerger only exports the fields that are required by the SAM file format; other user-defined fields included by the alignment program are discarded.

Guide to use of AgileSamFileMerger:

The AgileSamFileMerger user guide can be found here.


The AgileSamFileMerger program can be downloaded from my departments web site here.

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