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Hi @Sheila I was using the latest released version (3.4-46-gbc02625), but using a more recent nightly build (nightly-2015-10-26-g2bf3ff8) does solve the problem. Thanks!
I appear to have run into the same problem – regions with very high numbers of SNPs end up having no reads in the -bamout file, presumably because the region is not being processed. As in Kirstyn's post, this results in calls with almost no reads…