Hi Bioconductors,

Does the order of test and control bam files matters in shearwater??

How to specify that a certain file is either test or control file?

I defined test and control files as in shearwater manual as:

files<-c("test.bam","control.bam")

but in output vcf file it seems that REF and ALT columns were flipped over, so is it due to order of files?or due to another reason?

Thank you very much.