Filter out reads whose mate maps to a different contig

## Overview

This filter is intended to ensure that only reads that are likely to be mapped in the right place, and therefore to be informative, will be used in analysis. If mates in a pair are mapping to different contigs, it is likely that at least one of them is in the wrong place. One exception is you are using a draft genome assembly in which the chromosomes are fragmented into many contigs; then you may legitimately have reads that are correctly mapped but are on different contigs than their mate. This read filter can be disabled from the command line using the -drf argument.

#### Enable the bad mate filter

     java -jar GenomeAnalysisTk.jar \
-T ToolName \
-R reference.fasta \
-I input.bam \
-o output.file \


#### Disable the bad mate filter

     java -jar GenomeAnalysisTk.jar \
-T ToolName \
-R reference.fasta \
-I input.bam \
-o output.file \