I was calling SNP on mouse samples using GATK and was in the step of "Variant quality score recalibration". The VariantRecalibrator walker asked for training sets for mouse SNPs.
Does anyone know where to get those training files (specific for UCSC mm9 assembly)? Thanks!
Please provide sets of known polymorphic loci marked with the training=true ROD binding tag. For example, -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf
-resourcemni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf
-resourcemni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf
Comment