There seems to be a bug merging sam files when using splitting and BWA. The merge cats the files together and thus multiple headers are distributed through the file. Does anyone have plans to add a merge method to the SAM datatype class? Thanks, Ilya Ilya Chorny Ph.D. Bioinformatics Scientist I Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Work: 858.202.4582 Email: ichorny@illumina.com<mailto:ichorny@illumina.com> Website: www.illumina.com<http://www.illumina.com>