I have an annotated file, in which the last few columns is what the original VCF file would have. So I made a separate VCF file with just those columns, and uploaded them in Franklin with the approproiate HPO terms etc (germline variants, single case).
Issue is, Franklin keeps using hg19 as the reference genome, while I KNOW that the VCF and the annotated file are based on hg38. I contacted the helpline, where they say that it should take hg38 by default "if the VCF file is in standard format". There is no option to manually set the reference genome either.
Any help is appreciated, as this is my first stint with any bioinformatics.
Thank you!
Issue is, Franklin keeps using hg19 as the reference genome, while I KNOW that the VCF and the annotated file are based on hg38. I contacted the helpline, where they say that it should take hg38 by default "if the VCF file is in standard format". There is no option to manually set the reference genome either.
Any help is appreciated, as this is my first stint with any bioinformatics.
Thank you!