Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Detecting indels at sites of genome-editing by CRISPER/Cas9
Thank you for this great resource you have made available to the scientific community.
Background: We created targeted mutations in a human cell line using CRISPR/Cas9. We PCR amplified across the target site and sequenced the PCR product using ionTorrent. TMAP was used for alignment to hg19 and Integrated Genome Browser was used for viewing the alignments graphically. We can visualize deletions less than 30 bases but published literature indicates that we should see deletions and insertions around the cut site up to 150 bases (or even more). Some investigators have used a combination of bwa-mem with GATK for this purpose but they did not provide details of the analyses.
Clarification/query: Having have gone through the GATK tutorial videos (from March 2015) and perused GATK Best Practices, it appears that HC is the best tool for detecting larger indels. What parameters do I need to tweak in HC for this purpose.
I am surmising that I would also have to use the correct parameters in bwa-mem so that such deletions are in the output bam file for HC to be able to 'see' them.
I don't see a recommended pipeline for this type of analysis on the GATK website.
I also looked through all the 39 pages of Forum Pages but did not see this particular question being asked.