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!
Print Reads in GATK
I am unable to execute 'Print Reads' as I get the following error:
Unsupported CIGAR operator N in read read704 at chr21:33029208. Perhaps you are trying to use
RNA-Seq data? While we are currently actively working to support this data type unfortunately
the GATK cannot be used with this data in its current form. You have the option of either
filtering out all reads with operator N in their CIGAR string(please add --
filter_reads_with_N_cigar to your command line) or assume the risk of processing those reads as
they arre including the pertinent unsafe flag(please add -U ALLOW_N_CIGAR_READS to your command
line). Notice however that if you were to choose the latter, an unspecified subset of the
analytical outputs of an unspecified subset of the tools will become unpredictable. Consequently
the GATK team might well not be able to provide you with the usual support with any issue
regarding any output.
I tried both ways of filter option and allow cigar reads....but I still have the same error. Can you please help me in resolving this as soon as you can?
Thanks and Regards