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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