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Test-drive the GATK tools and Best Practices pipelines on Terra
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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