Shift, Add, and Drop From File
"From file" means that the regions selected to shift, add, or drop are specified from a provided file. These features provide the ability to finely control what regions are perturbed. For example, if you have a BED file specifying exon regions and you want to add only exons, you can use
Add from file example
bedshift -b mydata.bed -a 0.07 --addfile exons.bed
-a add rate will increase the size of
mydata.bed by 7% with new regions selected from
Shift from file example
Shift from file first calculates which regions overlap between the specified
--bedfile, then selects which regions to shift among those overlaps.
bedshift -b mydata.bed -s 0.42 --shiftmean 5 --shiftstdev 5 --shiftfile snp.bed
In this example, we only want to shift regions that are SNPs. The number of shifted regions is 42% of the total regions in
mydata.bed. Notice here that unlike
--addfile, we still have to specify the shift mean and standard deviation. This is because
--shiftfile tells which regions to shift, but not by how much.
Drop from file example
Drop from file, like shift from file, calculates overlaps between the specified
--bedfile, then selects regions from those overlaps to drop.
bedshift -b mydata.bed -d 0.4 -dropfile snp.bed
This command will drop regions that overlap with SNPs. The number of dropped regions is 40% of the total regions in