diff --git a/README.md b/README.md index c295cb1..f04e31f 100644 --- a/README.md +++ b/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.