add some docs on interpretation

README.md

@@ -41,6 +41,35 @@ duphold --threads 4 --vcf $svvcf --bam $cram --fasta $fasta --output $output.bcf
 
 the threads are decompression threads so increasing up to about 4 works.
 
+## Examples
+
+#### Duplication
+
+Here is a duplication with clear break-points (`DHD`) and clear
+change in depth (`DHBFC`)
+
+![image](https://user-images.githubusercontent.com/1739/45895409-5a224080-bd8e-11e8-844f-e7ffc13c7972.png "example IGV screenshot")
+
+`duphold` annotated this with
+
++ **DHD**: 2
++ **DHBFC**: 1.79
+
+where together these indicate rapid (DUP-like) change in depth at the break-points and a coverage that 1.79 times higher than the mean for the genome--again indicative of a DUP. Together, these recapitulate (or anticipate) what we see on visual inspection.
+
+#### Deletion
+
+A clear deletion will have rapid drop in depth at the left and increase in depth at the right and a lower mean coverage.
+
+![image](https://user-images.githubusercontent.com/1739/45895721-2dbaf400-bd8f-11e8-88b3-9fd5a90ef39e.png)
+
+`duphold` annotated this with:
+
++ **DHD**: -2
++ **DHBFC**: 0.6
+
+These indicate that both break-points are consistent with a deletion and that the coverage is ~60% of expected. So this is a clear deletion.
+
 ## Acknowledgements
 
 I stole the idea of annotating SVs with depth-change from Ira Hall.