I have bovine next generation sequence results from illumina miseq platform. In the data I have specific three genes. I need to do variantrecalibration, first what would I need to do this analysis? In the example command line, all the data sets origin is human since I am working with "nonhuman organism" I don't have every file on the list.
What information from the file would be essential for the VariantRecalibration step?
Also, I don't have the vcf file but one could be generated from the bovineHD SNP , so the generated file from bovineHD array manifest would be suitable to use for next generation sequence variantrecalibration analysis?