Changes

* --LDwindow specifies the length of the window that LD Matrix should be generated upon each variant. The default is 1MB.

* --LDwindow specifies the length of the window that LD Matrix should be generated upon each variant. The default is 1MB.

* --zip gives users the option of writing compressed files (bgzip compressed) automatically for convenient sharing.  

* --zip gives users the option of writing compressed files (bgzip compressed) automatically for convenient sharing.  

* --thin tells RAREMETALWORKER to thin points when generating QQ plot and Manhattan plots, so the file size is smaller.

* --thin tells RMW to thin points when generating QQ plot and Manhattan plots, so the file size is smaller.

* --labelHits tells RAREMETALWORKER to to label the hits using pvalue threshold 0.05/(#of variants tested) with gene name, based on human genome build 19.

* --labelHits tells RMW to to label the hits using pvalue threshold 0.05/(#of variants tested) with gene name, based on human genome build 19.

==== VC Options ====

==== VC Options ====