createGVCFfromMAF

fun createGVCFfromMAF(mafFile: String, referenceFile: String, gvcfOutput: String, sampleName: String, fillGaps: Boolean = false, twoGvcfs: Boolean = false, outJustGT: Boolean = false, outputType: MAFToGVCF.OUTPUT_TYPE = OUTPUT_TYPE.gvcf, compressAndIndex: Boolean = true, delAsSymbolic: Boolean = false, maxDeletionSize: Int = 0, anchorwaveLegacy: Boolean = false)

This method takes a mafFile and outputs a gvcf file to the specified path