I generated knock-out cell lines using CRISPR-Cas9 with 2 sgRNAs targeting 100bp apart. Then I identified knockout clones by PCR. Instead of sequencing all 75 clones, I decided to combine all clones together and send samples for targeted sequencing. I mapped the reads to the region of interest - instead of mapping to whole genome - using bwa mem default parameter. However instead of detecting deletion, bwa clipped the unmapped sequence. So my questions are,
1.Do you have any suggestions of which mapper I should use to detect 100bp deletion? It would be great if you have any suggestions for parameters to detect 100bp deletion.
2.Is there any software to identify how many different variants are in my samples?
Thanks in advance.