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first of all thanks for the support offered here. But (sadly) I have an other two questions.
I used the FastaAlternateReferenceMaker to create a consesus sequence and it worked great. Here I have a question regarding a warning: "IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation". I do not get this warning. Which dictionary is needed here. Is this warning comming up, because I used .gz and .tbi compressed vcf-files?
And a furhter question regarding the creation of a consesus sequence. I`m unsure what to do in cases of heterozygous INDELs. What would you suggest to do? Skip them as they are only represented by one allele or include them in the consensus. Both seems to be incorrect. Do you know the general handling here?