Is a vcf file necessary in IndelRealigner if we already used it to make intervals?

Question

[anp375]

I already used two vcf files to make intervals with RealignerTargetCreator. Do I really have to pass them in again to IndelRealigner or is it just an option to look at extra spots?

Answer 1

[mastal511]

It will probably throw an error if you don't pass them in again, as well as the intervals file.