We’re moving the GATK website, docs and forum to a new platform. Read the full story and breakdown of key changes on this blog.
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
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.
We will be out of the office for a Broad Institute event from Dec 10th to Dec 11th 2019. We will be back to monitor the GATK forum on Dec 12th 2019. In the meantime we encourage you to help out other community members with their queries.
Thank you for your patience!
Question Regarding GATK Doc #6483
I just happen to see a strange issue with this document.
In my own practice I always remove adapters at the very beginning (demultiplexing stage) and continue my analyses from fastq to uBAM to mapping and so on.
However recently I received some external data for analysis and realized that there is about 9 percent adapter contamination in fastqs. Looks like adapter cleanup is omitted in the demultiplexing stage.
As a personal preference I am against removing anything from fastq after demultiplexing stage and I am totally against trimmers since they tend to mess up with the order of reads and further complicate debugging of already established pipelines in production.
So I decided to give a try to MarkIlluminaAdapters option since that gives me the option to mark them and rescore them with QV2 therefore they won't interfere with my analyses. Looking at the document #6483 after marking illumina adapters step uBAM is streamed to BWA then streamed to MergeBamAlignment to create a clean bam however those marked adapters with QV2 are totally reverted to their original quality values (QV >30 for most!!!!) at that stage. So I am concerned about this.
Can anyone comment on that from GATK team why do we mark them if the original qualities will be restored anyway?
Am I missing something?
My current practice is to mark the adapters and convert uBAMxt to FASTQ with CLIPPING OPTION 2 and start mapping with this fastq and also generate a second uBAM with these new fastqs that contain the adapter sequences with QV2.
Am I understanding wrong?
Thanks for the help.