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