I am running the command:
igvtools count -w 1 --bases --query chr1:1326-1338 --minMapQuality 30 input.bam output.wig ref.fa
I get the correct number of A,C,G,T,N base counts as seen in IGV. However, I also need the number of insertions and deletions. They are shown in the GUI version, but I am unsure after looking at the documentation for igvtools count how to have it return these two values. I'm sure it's something simple I'm missing.
Any help you can provide would be appreciated.