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.

picard sortvcf

when I used GATK tool RealignerTargetCreator to realign my bam file to reference indel vcf files, it reports error that the two files have incompatible contigs. So I used picard ReorderSam and SortVcf to sort bam file and vcf file respectively. The SortVcf command reports error that "SAM dictionaries are not the same". How can I solve this error? thank you


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