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!
Error using SelectVariants
I constantly get this error ERROR MESSAGE: Input filesmgp.v3.indels.rsIDdbSNPv137.vcf and reference have incompatible contigs: Relative ordering of overlapping contigs differs, which is unsafe.
ERROR /mgp.v3.indels.rsIDdbSNPv137.vcf contigs = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, X]
ERROR reference contigs = [1, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 2, 3, 4, 5, 6, 7, 8, 9, MT, X, Y, JH584295.1, JH584292.1, GL456368.1, GL456396.1, GL456359.1, GL456382.1, GL456392.1, GL456394.1, GL456390.1, GL456387.1, GL456381.1, GL456370.1, GL456372.1, GL456389.1, GL456378.1, GL456360.1, GL456385.1, GL456383.1, GL456213.1, GL456239.1, GL456367.1, GL456366.1, GL456393.1, GL456216.1, GL456379.1, JH584304.1, GL456212.1, JH584302.1, JH584303.1, GL456210.1, GL456219.1, JH584300.1, JH584298.1, JH584294.1, GL456354.1, JH584296.1, JH584297.1, GL456221.1, JH584293.1, GL456350.1, GL456211.1, JH584301.1, GL456233.1, JH584299.1]
However, the file mentioned in the error (the one with less contigs) is actually downloaded from the Sanger institute website and according to their description it's based on the same mouse genome reference GRCm38. (available here: ftp://ftp-mouse.sanger.ac.uk/REL-1303-SNPs_Indels-GRCm38).
I really am looking forward to your answer!
Thanks in advance!
P.S. changing the header didn't help ... and using SortVcf gave the following error:
"Exception in thread "main" java.lang.UnsupportedClassVersionError: picard/cmdline/PicardCommandLine : Unsupported major.minor version 52.0" ....