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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.

Unable to use VariantRecalibrator

Hi everyone, I am very new in the field of bioinformatics. Currently, I am working with whole Genome Sequencing Dataset. I am working with mouse data. I am stuck with the VariantRecalibrator steps. Where could I find the data for mouse to train the model? For example this one is the example for human data which is in the GATK website. -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf \ -resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf \ -resource:1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.high_confidence.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_135.b37.vcf \ But I need something very similar for mouse.Could you please help to to get it through. Thank you in advance. Sincerely, Santosh


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