export your bam as SAM and use awk to filter the result (something like

awk '($3!=$7 && $7!="=")'

). The SAM specification ( samtools.sourceforge.net/SAM1.pdf ) says that the column $3 is the CHROMOSOME and the $7 is the chromosome for the mate

Here is a simple method:

samtools view -F 14 infile.bam | grep -v " = " > outfile.sam

The -F 14 gives you reads that are

• are mapped
• have a mate that is mapped
• but are not mapped in a proper pair

Note that there are TAB characters left and right of the = sign. Try Ctrl-V [HTML] to enter them at the terminal.

can be shortened to (including mapQ>5):

samtools view -F 14 -q 5 -h input.sam \
    | awk '$7 !~ /=/' \
    | samtools view -Sb - \
    > map_2_diff_chroms.bam