Closed carlyprior closed 6 years ago
The VCF format requires a reference. You need some coordinate system to place variants on.
I see. I don't have a reference genome so is there a way to use the output from bubbles to get a VCF? Sorry for my misunderstanding about calls2vcf.
You could have a fake reference where each bubble has its own chromosome number. Assume each chromosome starts at the beginning of the flank.
I'm struggling to figure out how to run the calls2vcf command without a reference. I see that you need a 5' flank file in SAM or BAM format, but it is unclear how I am to achieve this without a reference as both BWA and Stampy require references.