Modified SID settings to allow up to 10k coverage and lowered AF thresho...

...ld to 0.5%

Hi Brad,
I've made some modifications to how SID is called, namely I'm adjusting ```maxNumberOfReads``` to accommodate downsampling, which I've limited to 10k max. This helps in not discarding windows with high coverage panels. 

Further I fixed a typo on line 121 where I was not passing the region to the merging algorithm. SID has a funny habit of reporting indels outside the specified interval so passing the region to merging parses these InDels out and avoids out-of-order errors downstream.

I've fixed minimum reportable AF to 0.5% for now but I'd be very happy to expose this setting to the user in the sample config, what do you think?