Not a question - just found out how to do this and I don't think this is particularly well documented, so just posting this here to help other users.
To compare several BAM files in Artemis, first load one BAM file (File > Read BAM / VCF), then right-click in the BAM window and choose "Add BAM". The reads from the two BAM files will be merged into the one window, so the trick is to right-click again and select "Clone Window".
Now you have two BAM windows with the same merged reads view. Right-click into each one individually and choose "BAM files", which brings up a tick-box list of the loaded files. Now select a different active BAM file in each window to end up with two windows, each showing only the reads from a single BAM file.
To compare several BAM files in Artemis, first load one BAM file (File > Read BAM / VCF), then right-click in the BAM window and choose "Add BAM". The reads from the two BAM files will be merged into the one window, so the trick is to right-click again and select "Clone Window".
Now you have two BAM windows with the same merged reads view. Right-click into each one individually and choose "BAM files", which brings up a tick-box list of the loaded files. Now select a different active BAM file in each window to end up with two windows, each showing only the reads from a single BAM file.
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