Ordering the sequence reads in a *.sam file by chromosome and map position

AgileSAMFileSorter reads the sequence reads in an unsorted *.sam file and creates a second *.sam file in which all the sequence reads are sorted by chromosome number and position. Reads that are not mapped to the reference sequence are discarded. However, reads that are duplicates of another read will be retained.

AgileSAMFileSorter 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 AgileSAMFileSorter

The AgileSAMFileSorter user guide can be found here.


The AgileSAMFileSorter program can be downloaded here.

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