hammerlab/guacamole — pull request #170 by arahuja (2014-09-12 17:40:44+00:00)
Title: Move removing nearby or correlated snps to second pass

Final piece of #147 pulled out - includes #163 but will rebase once that is merged in

- Removed check for correlated (nearby) SNVs from caller - moved this to a second pass over genotypes in some window
- Adding average mapping quality filter
- Adding average base quality filter