Hello and thank you in advance for any assistance with my problem.
I am working with a dCas9-deaminase base editor and I am trying to assay the off-target effects of the enzyme. Usually, I would use the VCF file from my alignments, however, in this case, my sequencing is not clonal.
To be more specific, I induced expression of dCas9-deaminase in my culture for 6 hours and then performed WGS of the whole mutated culture. I expect to see some baseline level of random mutations across the genome as well as hotspots of elevated mutations.
Previously, I've used bwa to align reads and used my sorted and indexed bam file as input to the program bam-readcount (https://github.com/genome/bam-readcount) to count the frequency of mutation at each genomic position. I'm hoping to find something that can essentially do this for me.
I'm also interested in packages I could use to visualize my results. I greatly prefer python over R.
Thank you!
