Add soft filter by region

[yjqiu]

I would like to add soft filter based on regions from a bed file. However, with -R options. the sites outside the region will be removed. With expression, it will only work for a single region instead of multiple regions.

[pd3]

This is now supported, please check the new --mask-file option

[yjqiu]

Thanks for the support! Just to confirm, I didn't see the option in 1.14. Is it only in the GitHub for now? @pd3

[pd3]

Yes, only in git for now, http://samtools.github.io/bcftools/howtos/install.html