On Mon, May 13, 2013 at 3:21 PM, Janier J. Ramírez <jjramirez at estudiantes.uci.cu> wrote: > There is in Biojava a parser for some of the next file formats ?? : > .sam > .bam > ... I'm not sure what exactly is in BioJava for these formats, but I would suggest you (also) consider Picard for working with SAM/BAM in Java. Peter