Missing/masked intervals

[soisa001]

Hello,

In the current implementation it does not appear that phlash can handle large missing windows (seems like it can result in strange inference times). Is there a way to easily specify masked intervals (e.g. genic regions, centromeres) that should be excluded from the analysis? e.g. I believe gamma-smc has this functionality. I am using vcfs of chr1-22.

Thanks,
Natthapon