Getting the coordinates of targeted locations by sgRNAs

Question

[Sara]

I have performed CRISPR-CAS9 exprimrnt which was followed by WGS. now I am trying to find the locations that are targeted by the sgRNAs. do you the steps that I should follow or the tools that I can use? so far I aligned the reads to the reference genome and have the bam files.

[ATpoint]

Some more details are necessary. Is this a knockout attempt with two gRNAs flanking a certain region or was a new piece of DNA introduced or was introduction of SNPs the goal? Essentially, what is the trace your Cas9 is supposed to leave in the genome?

[Sara]

@ATpoint: basically we have used this technique to find the structural variants at the off-target sites.

[ATpoint]

So not really related to CRISPR but rather normal WGS and SV scanning. Then it comes down to using any structural variant caller to find SVs. Prominent choices could be Lumpy, Manta, Pindel and many more. Please browse this forum and the web for tools and benchmarks.