Trying to get my PHG imputation pipeline running.
In the configuration file example for "imputing haplotypes from variants in a VCF file", one parameter is
Where should I derive this vcfIndexFile?
Or, is it generated by the pipeline (it is located in the outputDir, so maybe?)
inputType=vcf keyFile=/phg/readMapping_key_file.txt readMethod=**UNASSIGNED** vcfDir=/phg/inputDir/imputation/vcf/ countAlleleDepths=true
readMethod required? Here, I want to use variants in a vcf, so no reads are being used, I think? So do I need this parameter, or the
Sorry if I am misunderstanding obvious points.